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As of 14-Apr-2021 number of released structures: 11277
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Polymer Type: All + Protein Function: All + Structural Features: All + Experimental Method: All

Results: 7637  Download results as an excel file       Gallery view

NDB ID:

 6YL2

PDB ID:

6YL2 

Release:

2021-04-14

Title:

Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism

Classification:

DNA BINDING PROTEIN

Authors:

Pritchard, J.E., Sula, A., Cole, A.R., Kendall, S.L., Keep, N.H.

Citation:

Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.15Å R work:0.267R free:0.284

NDB ID:

 7DKG

PDB ID:

7DKG 

Release:

2021-04-14

Title:

Influenza H5N1 nucleoprotein (truncated) in complex with nucleotides

Classification:

VIRAL PROTEIN/RNA

Authors:

Tang, Y.S., Xu, S., Chen, Y.W., Wang, J.H., Shaw, P.C.

Citation:

Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.288R free:0.331

NDB ID:

 7DXP

PDB ID:

7DXP 

Release:

2021-04-14

Title:

Influenza H5N1 nucleoprotein in complex with nucleotides

Classification:

VIRAL PROTEIN/RNA

Authors:

Tang, Y.S., Xu, S., Chen, Y.W., Wang, J.H., Shaw, P.C.

Citation:

Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.193R free:0.248

NDB ID:

 7BIL

PDB ID:

7BIL 

Release:

2021-04-07

Title:

Crystal structure of helicase Pif1 from Thermus oshimai in complex with oligo GGTTTGGTTTGGTT

Classification:

HYDROLASE

Authors:

Dai, Y.X., Chen, W.F., Liu, N.N., Teng, F.Y., Guo, H.L., Hou, X.M., Dou, S.X., Rety, S., Xi, X.G.

Citation:

Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.21Å R work:0.179R free:0.22

NDB ID:

 7E4E

PDB ID:

7E4E 

Release:

2021-04-07

Title:

NMR solution structures of DNA minidumbbell containing a N1-methyladenine

Classification:

DNA

Authors:

Wan, L., Lam, S.L., Lee, H.K., Guo, P.

Citation:

Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 7LUF

PDB ID:

7LUF 

Release:

2021-04-07

Title:

HSV1 polymerase ternary complex with dsDNA and PNU-183792

Classification:

Transferase/DNA

Authors:

Hayes, R.P., Heo, M., Mason, M., Reid, J., Burlein, C., Armacost, K.A., Tellers, D.M., Raheem, I., Shaw, A.W., Murray, E., McKenna, P.M., Abeywickrema, P., Sharma, S., Soisson, S.M., Klein, D.

Citation:

Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.5Å R work:0.225R free:0.245

NDB ID:

 7NBK

PDB ID:

7NBK 

Release:

2021-04-07

Title:

Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Classification:

DNA

Authors:

Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

Citation:

Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7NBL

PDB ID:

7NBL 

Release:

2021-04-07

Title:

Solution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Classification:

DNA-RNA HYBRID

Authors:

Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

Citation:

Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7NEJ

PDB ID:

7NEJ 

Release:

2021-04-07

Title:

Solution structure of DNA:RNA hybrid duplex

Classification:

DNA-RNA HYBRID

Authors:

Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

Citation:

Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 6UG1

PDB ID:

6UG1 

Release:

2021-03-31

Title:

Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Paul, D., Min, J.-H.

Citation:

Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex
To be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.833Å R work:0.224R free:0.271

NDB ID:

 6W9P

PDB ID:

6W9P 

Release:

2021-03-31

Title:

Tel26 Parallel Four-quartet G-quadruplex with K+

Classification:

DNA

Authors:

McCarthy, S.E., Yatsunyk, L.A., Beseiso, D., Miao, J.

Citation:

Structural diversity and ligand binding of G-rich DNA from telomeric region of Tetrahymena thermophila
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.99Å R work:0.196R free:0.209

NDB ID:

 6WQU

PDB ID:

6WQU 

Release:

2021-03-31

Title:

CSL (RBPJ) bound to Notch3 RAM and DNA

Classification:

TRANSCRIPTION/SIGNALING PROTEIN/DNA

Authors:

Landor, S.K.J., Santio, N.M., Eccleshall, W.B., Paramonov, V.M., Gagliani, E.K., Hall, D., Jin, S.B., Dahlstrom, K.M., Salminen, T.A., Rivero-Muller, A., Lendahl, U., Kovall, R.A., Koskinen, P.J., Sahlgren, C.

Citation:

PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion.
J.Biol.Chem. pp.100593 - 100593 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.41Å R work:0.198R free:0.233

NDB ID:

 7AMN

PDB ID:

7AMN 

Release:

2021-03-31

Title:

Structure of LuxR with DNA (repression)

Classification:

TRANSCRIPTION

Authors:

Zhang, J., Liu, B., Gu, D., Hao, Y., Chen, M., Ma, Y., Zhou, X., Reverter, D., Zhang, Y., Wang, Q.

Citation:

Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression.
Nucleic Acids Res. 49 pp.3274 - 3293 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.209R free:0.242

NDB ID:

 7AMT

PDB ID:

7AMT 

Release:

2021-03-31

Title:

Structure of LuxR with DNA (activation)

Classification:

TRANSCRIPTION

Authors:

Zhang, J., Liu, B., Gu, D., Hao, Y., Chen, M., Ma, Y., Zhou, X., Reverter, D., Zhang, Y., Wang, Q.

Citation:

Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression.
Nucleic Acids Res. 49 pp.3274 - 3293 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.22R free:0.249

NDB ID:

 7CR6

PDB ID:

7CR6 

Release:

2021-03-31

Title:

Synechocystis Cas1-Cas2/prespacer binary complex

Classification:

IMMUNE SYSTEM/DNA

Authors:

Wu, C., Tang, D., Cheng, J., Hu, D., Yang, Z., Ma, X., He, H., Yao, S., Fu, T.M., Yu, Y., Chen, Q.

Citation:

Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis.
Nucleic Acids Res. 49 pp.2973 - 2984 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.72Å R work:0.275R free:0.324

NDB ID:

 7CR8

PDB ID:

7CR8 

Release:

2021-03-31

Title:

Synechocystis Cas1-Cas2-prespacerL complex

Classification:

IMMUNE SYSTEM/DNA

Authors:

Wu, C., Tang, D., Cheng, J., Hu, D., Yang, Z., Ma, X., He, H., Yao, S., Fu, T.M., Yu, Y., Chen, Q.

Citation:

Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis.
Nucleic Acids Res. 49 pp.2973 - 2984 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.7Å R work:0.295R free:0.34

NDB ID:

 7CUK

PDB ID:

7CUK 

Release:

2021-03-31

Title:

Structure of a GG mismatch-containing duplex formed by G4C2 repeats

Classification:

DNA

Authors:

Maity, A., Winnerdy, F.R., Chen, G., Phan, A.T.

Citation:

Duplexes Formed by G 4 C 2 Repeats Contain Alternate Slow- and Fast-Flipping G·G Base Pairs.
Biochemistry pp. - 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7ADU

PDB ID:

7ADU 

Release:

2021-03-24

Title:

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ440 (compound 5j)

Classification:

VIRAL PROTEIN

Authors:

Smith, S.J., Zhao, X.Z., Passos, D.O., Pye, V.E., Cherepanov, P., Lyumkis, D., Burke Jr., T.R., Hughes, S.H.

Citation:

HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants.
Acs Infect Dis. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.62Å R work:0.202R free:0.231

NDB ID:

 7ADV

PDB ID:

7ADV 

Release:

2021-03-24

Title:

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ447 (compound 6v)

Classification:

VIRAL PROTEIN

Authors:

Smith, S.J., Zhao, X.Z., Passos, D.O., Pye, V.E., Cherepanov, P., Lyumkis, D., Burke Jr., T.R., Hughes, S.H.

Citation:

HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants.
Acs Infect Dis. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.65Å R work:0.195R free:0.219

NDB ID:

 7JM4

PDB ID:

7JM4 

Release:

2021-03-24

Title:

IRF Transcription Factor

Classification:

TRANSCRIPTION

Authors:

Sundararaj, S., Seneviratne, S., Williams, S.J., Enders, A., Casarotto, M.G.

Citation:

Structural determinants of the IRF4/DNA homodimeric complex.
Nucleic Acids Res. 49 pp.2255 - 2265 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.95Å R work:0.184R free:0.205

NDB ID:

 7JNP

PDB ID:

7JNP 

Release:

2021-03-24

Title:

MtrR bound to the rpoH operator from Neisseria gonorrhoeae

Classification:

DNA BINDING PROTEIN

Authors:

Beggs, G.A., Ayala, J., Kavanagh, L.G., Read, T.D., Hooks, G.M., Schumacher, M.A., Shafer, W.M., Brennan, R.G.

Citation:

Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.198R free:0.256

NDB ID:

 7JU3

PDB ID:

7JU3 

Release:

2021-03-24

Title:

MtrR bound to the mtrCDE operator from Neisseria gonorrhoeae

Classification:

DNA BINDING PROTEIN

Authors:

Beggs, G.A., Ayala, J., Kavanagh, L.G., Read, T.D., Hooks, G.M., Schumacher, M.A., Shafer, W.M., Brennan, R.G.

Citation:

Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.227R free:0.282

NDB ID:

 6W5X

PDB ID:

6W5X 

Release:

2021-03-17

Title:

Crystal structure of human polymerase eta complexed with N7-benzylguanine and dCTP*

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Jung, H., Lee, S.

Citation:

Crystal structure of human polymerase eta complexed with N7-benzylguanine and dCTP*
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.59Å R work:0.184R free:0.255

NDB ID:

 7K30

PDB ID:

7K30 

Release:

2021-03-17

Title:

Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dU at the active site

Classification:

HYDROLASE/DNA

Authors:

Shi, K., Moeller, N.H., Banerjee, S., McCann, J.L., Carpenter, M.A., Yin, L., Moorthy, R., Orellana, K., Harki, D.A., Harris, R.S., Aihara, H.

Citation:

Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.34Å R work:0.205R free:0.228

NDB ID:

 7K31

PDB ID:

7K31 

Release:

2021-03-17

Title:

Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dI at the active site

Classification:

HYDROLASE/DNA

Authors:

Shi, K., Moeller, N.H., Banerjee, S., McCann, J.L., Carpenter, M.A., Yin, L., Moorthy, R., Orellana, K., Harki, D.A., Harris, R.S., Aihara, H.

Citation:

Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.88Å R work:0.182R free:0.238

NDB ID:

 7K32

PDB ID:

7K32 

Release:

2021-03-17

Title:

Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site

Classification:

HYDROLASE/DNA

Authors:

Shi, K., Moeller, N.H., Banerjee, S., McCann, J.L., Carpenter, M.A., Yin, L., Moorthy, R., Orellana, K., Harki, D.A., Harris, R.S., Aihara, H.

Citation:

Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.11Å R work:0.199R free:0.247

NDB ID:

 7K33

PDB ID:

7K33 

Release:

2021-03-17

Title:

Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site

Classification:

HYDROLASE/DNA

Authors:

Shi, K., Moeller, N.H., Banerjee, S., McCann, J.L., Carpenter, M.A., Yin, L., Moorthy, R., Orellana, K., Harki, D.A., Harris, R.S., Aihara, H.

Citation:

Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.11Å R work:0.19R free:0.229

NDB ID:

 6ZX6

PDB ID:

6ZX6 

Release:

2021-03-10

Title:

Antiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter containing 8-oxoG

Classification:

DNA

Authors:

Bielskute, S., Plavec, J., Podbevsek, P.

Citation:

Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter.
Nucleic Acids Res. 49 pp.2346 - 2356 2021

Experiment:

 SOLUTION NMR

NDB ID:

 6ZX7

PDB ID:

6ZX7 

Release:

2021-03-10

Title:

Antiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter

Classification:

DNA

Authors:

Bielskute, S., Plavec, J., Podbevsek, P.

Citation:

Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter.
Nucleic Acids Res. 49 pp.2346 - 2356 2021

Experiment:

 SOLUTION NMR

NDB ID:

 7D98

PDB ID:

7D98 

Release:

2021-03-10

Title:

Crystal structure of full-length CbnR complexed with the target DNA complex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Giannopoulou, E.A., Senda, M., Koentjoro, M.P., Adachi, N., Ogawa, N., Senda, T.

Citation:

Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA.
Febs J. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.6Å R work:0.234R free:0.286

NDB ID:

 6LER

PDB ID:

6LER 

Release:

2021-03-03

Title:

169 bp nucleosome harboring non-identical cohesive DNA termini.

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

169 bp nucleosome harboring non-palindromic DNA with cohesive ends.
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.208R free:0.26

NDB ID:

 7B1Y

PDB ID:

7B1Y 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR complexed with cobalt and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.12Å R work:0.229R free:0.252

NDB ID:

 7B20

PDB ID:

7B20 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR complexed with iron and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.18Å R work:0.209R free:0.245

NDB ID:

 7B23

PDB ID:

7B23 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR complexed with cobalt and the SACE_2689 promoter DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.15Å R work:0.226R free:0.247

NDB ID:

 7B24

PDB ID:

7B24 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR (P39G variant) complexed with cobalt and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.05Å R work:0.225R free:0.258

NDB ID:

 7B25

PDB ID:

7B25 

Release:

2021-03-03

Title:

DtxR-like iron-dependent regulator IdeR (Q43A variant) complexed with cobalt and its consensus DNA-binding sequence

Classification:

TRANSCRIPTION

Authors:

Marcos-Torres, F.J., Maurer, D., Griese, J.J.

Citation:

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout
Biorxiv pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.34Å R work:0.267R free:0.283

NDB ID:

 7BPV

PDB ID:

7BPV 

Release:

2021-03-03

Title:

r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid duplex structure

Classification:

DNA-RNA HYBRID

Authors:

Wang, S.C., Satange, R.B., Hou, M.H.

Citation:

r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid structure
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.781Å R work:0.217R free:0.237

NDB ID:

 7K5O

PDB ID:

7K5O 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 1 min post dATP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.16Å R work:0.186R free:0.226

NDB ID:

 7K5P

PDB ID:

7K5P 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 4 min post dATP addition

Classification:

TRANSFERASE

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.97Å R work:0.219R free:0.257

NDB ID:

 7K5Q

PDB ID:

7K5Q 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 8 min post dATP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.193R free:0.246

NDB ID:

 7K5R

PDB ID:

7K5R 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 120 min post dATP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.188R free:0.238

NDB ID:

 7K5S

PDB ID:

7K5S 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 4 hr post dATP and dCTP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.67Å R work:0.186R free:0.209

NDB ID:

 7K5T

PDB ID:

7K5T 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 25.5 hr post dATP and dCTP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.3Å R work:0.19R free:0.236

NDB ID:

 7K5U

PDB ID:

7K5U 

Release:

2021-03-03

Title:

Bst DNA polymerase I time-resolved structure, 48 hr post dATP and dCTP addition

Classification:

TRANSFERASE/DNA

Authors:

Chim, N., Meza, R.A., Trinh, A.M., Yang, K., Chaput, J.C.

Citation:

Visualizing DNA Synthesis by a Replicative DNA Polymerase
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.189R free:0.229

NDB ID:

 7LFQ

PDB ID:

7LFQ 

Release:

2021-03-03

Title:

Pyrococcus RNA ligase

Classification:

LIGASE/DNA

Authors:

Banerjee, A., Goldgur, Y., Shuman, S.

Citation:

Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide.
Rna pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.191R free:0.216

NDB ID:

 6WJK

PDB ID:

6WJK 

Release:

2021-02-24

Title:

Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry

Classification:

DNA

Authors:

Simmons, C.R., MacCulloch, T., Zhang, F., Liu, Y., Stephanopoulos, N., Yan, H.

Citation:

A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Angew.Chem.Int.Ed.Engl. 59 pp.18619 - 18626 2020

Experiment:

 X-RAY DIFFRACTION Resolution:4.514Å R work:0.197R free:0.242

NDB ID:

 6L9Z

PDB ID:

6L9Z 

Release:

2021-02-17

Title:

338 bp di-nucleosome assembled with linker histone H1.X

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

Dinucleosome 338 bp with linker histone H1.X
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.203R free:0.256

NDB ID:

 6LA2

PDB ID:

6LA2 

Release:

2021-02-17

Title:

343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

Dinucleosome 338 bp with linker histone H1.X
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.89Å R work:0.199R free:0.266

NDB ID:

 6LAB

PDB ID:

6LAB 

Release:

2021-02-17

Title:

169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0

Classification:

DNA BINDING PROTEIN

Authors:

Sharma, D., Davey, C.A., Adhireksan, Z.

Citation:

Nucleosome 169 bp with linker histone H1.0
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.2Å R work:0.208R free:0.263

NDB ID:

 6VUG

PDB ID:

6VUG 

Release:

2021-02-17

Title:

Diabody bound to a Reverse Transcriptase Aptamer Complex

Classification:

PROTEIN BINDING

Authors:

Chesterman, C., Arnold, E.

Citation:

Co-crystallization with diabodies: a case study for the introduction of synthetic symmetry.
Structure pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.202R free:0.254

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