NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 3. April 1992. C------W C------W C--------W NNN NNN DDDDDD BBBBBBB C--------W C--------W NNNN NNN DDDDDDDD BBBBBBBBB C--------W C-------W NNNNN NNN DDD DDD BBB BBB C-------W C----W NNN NN NNN DDD DDD BBBBBBB C----W W NNN NNNNN DDD DDD BBB BBB W W--C NNN NNNN DDDDDDDD BBBBBBBBB W--C W-----C NNN NNN DDDDDD BBBBBBB W-----C W--------C W--------C W---------C W---------C W--------C W--------C W-----C THE NUCLEIC ACID DATABASE: W-----C C -------------------------- C C--W C--W C------W A RELATIONAL DATABASE OF NUCLEIC C------W C--------W ACID CRYSTAL STRUCTURES C--------W C--------W C--------W INTRODUCTION: ------------ This third newsletter of the Nucleic Acid Database updates the information and data presented in the second newsletter, in February, 1992. Since then, seven new DNA, one RNA, and ten tRNA structures have been added to the database. New coordinates are available for 19 DNA and eight tRNA structures. The current release consists of updated tables describing the 192 DNA, RNA, and tRNA structures now contained in the database, and coordinate files for all structures, where coordinates are available. The Nucleic Acid Database Project represents a collaborative effort between Helen Berman and Wilma Olson of Rutgers University and David Beveridge of Wesleyan University, and is funded by the Division of Instrumentation and Resources of the National Science Foundation (DIR 90 12772). If you use the tables, please use the following citation: The Nucleic Acid Database: A Guide to the Use of a Relational Database of Nucleic Acid Crystal Structures, 1991. Technical Report. Helen M. Berman, Wilma K. Olson, John Westbrook, Anke Gelbin, Tamas Demeny, Shu-Hsin Hsieh, Center for Computational Chemistry, Rutgers University, New Brunswick, NJ and David L. Beveridge, Wesleyan University, Middletown, CN. Page 2 WHAT IS NEW? ------------ 1. NEW STRUCTURES: The following new DNAs and RNAs have been added to NDB: ARL037 5'-R(*GP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*C)-3' BDL034 5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3', -15 C BDL035 5'-D(*AP*CP*CP*GP*CP*CP*GP*GP*CP*GP*CP*C)-3', -15 C DDF031 5'-D(*TP*GP*TP*AP*CP*A)-3', DAUNOMYCIN DDF032 5'-D(*TP*GP*AP*TP*CP*A)-3', DAUNOMYCIN UDM017 5'-D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', SOAKED W/PROFLAVIN ZDH030 5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3' ZDFB31 5'-D(*CP*GP*UP*(NH2)AP*CP*G)-3' 2. NEW COORDINATES: Coordinates for the following structures have been released: ADL025 5'-D(*CP*CP*CP*CP*CP*GP*CP*GP*GP*GP*GP*G)-3', SPERMINE BDJ019 5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*)-3' BDJ025 5'-D(*CP*GP*AP*TP*CP*GP*AP*TP*CP*G)-3' BDJB27 5'-D(*CP*CP*AP*GP*GP*CP*(M)CP*TP*GP*G)-3' BDL029 5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3' DDF023 5'-D(*CP*GP*CP*GP*CP*G)-3', DAUNORUBICIN (DAUNOMYCIN) AND HCHO DDF026 5'-D(*CP*GP*TP*AP*CP*G)-3', MAR70 DDF028 5'-D(*CP*GP*AP*TP*CP*G)-3', 4-O-DEMETHYL-11-DEOXYDOXORUBICIN (ddDOX) DDF029 5'-D(*CP*GP*AP*TP*CP*G)-3', IDARUBICIN (4-METHOXY-DAUNORUBICIN) (IDR) DDFB24 5'-D(*CP*GP*TP*(NH2)AP*CP*G)-3', DAUNORUBICIN (DAUNOMYCIN) AND HCHO DDFB25 5'-D(*CP*GP*TP*(NH2)AP*CP*G)-3', MAR70 AND HCHO GDL008 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', 4'-6-DIAMIDINE-2-PHENYL INDOLE (DAPI) GDL010 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33258, 0 C, PIPERAZINE UP GDL011 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33258, 0 C, PIPERAZINE DOWN GDL012 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33258, -25 C, PIPERAZINE DOWN GDL013 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33258, -100 C, PIPERAZINE DOWN ZDF028 5'-D(*CP*GP*CP*GP*CP*G)-3', COPPER(II) CHLORIDE SOAKED ZDF029 5'-D(*CP*GP*CP*GP*CP*G)-3', SPERMINE ZDFB10 5'-D(*(M)CP*GP*UP*AP*(M)CP*G)-3', COPPER(II) CHLORIDE SOAKED Page 3 3. TRANSFER-RNAs: The following new tRNAs have been added to NDB: TRNA01 TRANSFER RIBO-NUCLEIC ACID (YEAST, PHE), T-RNA TRNA02 PB(II)-TRANSFER RIBO-NUCLEIC ACID (YEAST,PHE) T-RNA (PH 7.4) TRNA03 PB(II)-TRANSFER RIBO-NUCLEIC ACID (YEAST,PHE) T-RNA (PH 5.0) TRNA04 TRANSFER RIBO-NUCLEIC ACID (YEAST,PHE),T-RNA TRNA05 TRANSFER RIBO-NUCLEIC ACID (YEAST,ASP) T-RNA TRNA06 TRANSFER RIBO-NUCLEIC ACID (YEAST, PHE), T-RNA TRNA07 TRANSFER RIBO-NUCLEIC ACID (YEAST,ASP) T-RNA (A FORM) TRNA08 TRANSFER RIBO-NUCLEIC ACID (YEAST,ASP) T-RNA (B FORM) TRNA09 TRANSFER RIBO-NUCLEIC ACID (YEAST,PHE),T-RNA TRNA10 TRANSFER RIBO-NUCLEIC ACID (YEAST,PHE) T-RNA All of these structures, except TRNA01 and TRNA02, have coordinates 4. GRAPHICS: TORSION ANGLE CONFORMATION RINGS: PostScript graphics files containing conformation rings (1) depicting the occurrences of nucleic acid backbone and side group torsion angles {P-O5' alpha (omega), O5'-C5' beta (phi), C5'-C4' gamma (psi), C4'-C3' delta (psi prime), C3'-O3' epsilon (phi prime), O3'-P zeta (omega prime), C1'-N glycosyl chi} corresponding to the different DNA and RNA structures present in the Nucleic Acid Database have been recently put into the electronic library. The conformation rings describe the occurrences of the six backbone torsion angles and the glycosyl rotation of the various DNAs and RNAs in a series of concentric rings. The NDB file name is indicated at the bottom of each figure. Each ring is labeled from 0 degrees to 360 degrees and the occurrence of a particular torsion angle is noted by a radial line in the appropriate angular location. Multiple lines in a given ring represent the various values of a particular torsion of the selected structure. The sectors with dense lines readily reveal the preferred conformation range of the corresponding torsions. The distribution of radial lines in a given ring reflects the flexibility of the specified torsion. Dark and light shadings are respectively used to highlight states within one and two standard deviation units of the mean. Outlying torsions are thereby immediately detectable. Visual comparison of the approximate preferences and the flexibility of different torsion angles is also made easy by the patterns of lines in different concentric rings. Comparisons of the conformation rings of different structures provide direct information on their overall similarities and differences. (1) A. R. Srinivasan and Wilma K. Olson, Nucleic Acids Research, 8, 2307-2329 (1980). Page 4 These files have names in the following format: ring_.ps where the word is substituted by the NDB File Name of the structure desired. These files, together with the tables containing torsion angles, have been put into the library called 'torsions'. For detailed instructions on how to obtain these files, refer below, to the ACCESS INFORMATION section of this newsletter. 5. UPDATED TABLES: All the originally released tables have been updated to include information about the newly added structures. 6. SUBSCRIPTIONS: To subscribe to the Nucleic Acid Database mailing list, send the following mail message: To: ndblib@helix.rutgers.edu Subject: subscribe To subscribe for someone else, send a mail message to ndbadmin@helix.rutgers.edu indicating the person's name and electronic mail address. Page 5 STAFF OF THE NUCLEIC ACID DATABASE PROJECT: ------------------------------------------ Helen M. Berman, Wilma K. Olson, David L. Beveridge--Principal Investigators John Westbrook--Director, Center for Computational Chemistry, Rutgers University Anke Gelbin--Database Coordinator Tamas Demeny--Database Programmer Shuhsin Hsieh--Database Programmer Page 6 ACCESS INFORMATION: ------------------ The released information is located in the NUCLEIC ACID DATABASE LIBRARY (NDBLIB). The library is divided into the following directories: newsletter reports_ascii reports_ps coordinates torsions You can communicate with this library in two ways: 1. ELECTRONIC MAIL (MAIL SERVER) 2. FILE TRANSFER PROGRAM (ANONYMOUS FTP) 1. MAIL SERVER INSTRUCTIONS: The electronic mail address of NDBLIB is: Internet: ndblib@helix.rutgers.edu To obtain general information about NDBLIB, send the following mail message: To: ndblib@helix.rutgers.edu Subject: send index To obtain information about a particular directory, send this message: To: ndblib@helix.rutgers.edu Subject: send index from Where is substituted by one of the names listed above. If you have never received a newsletter before, send the following message for complete access instructions: To: ndblib@helix.rutgers.edu Subject: send access from newsletter 2. ANONYMOUS FTP: Address: helix.rutgers.edu Username: anonymous Password: