Header list of 1bps.pdb file
Complete list - 3 202 Bytes
HEADER DNA 06-AUG-98 1BPS
TITLE MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN
TITLE 2 DUPLEX DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*CP*(BAP)AP*CP*GP*AP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10-
COMPND 6 TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6
COMPND 7 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH
COMPND 8 TRANS ADDITION AT THE C10 OF THE EPOXIDE.;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3');
COMPND 11 CHAIN: B;
COMPND 12 ENGINEERED: YES;
COMPND 13 OTHER_DETAILS: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 8 ORGANISM_TAXID: 32630
KEYWDS DEOXYRIBONUCLEIC ACID, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, DUPLEX
KEYWDS 2 DNA, DNA
EXPDTA SOLUTION NMR
AUTHOR J.S.SCHWARTZ,J.S.RICE,B.A.LUXON,J.M.SAYER,G.XIE,H.J.C.YEH,X.LIU,
AUTHOR 2 D.M.JERINA,D.G.GORENSTEIN
REVDAT 6 03-NOV-21 1BPS 1 SOURCE REMARK LINK
REVDAT 5 24-FEB-09 1BPS 1 VERSN
REVDAT 4 01-APR-03 1BPS 1 JRNL
REVDAT 3 26-SEP-01 1BPS 3 ATOM CONECT
REVDAT 2 29-DEC-99 1BPS 4 HEADER COMPND REMARK JRNL
REVDAT 2 2 4 ATOM SOURCE SEQRES
REVDAT 1 19-AUG-98 1BPS 0
JRNL AUTH J.L.SCHWARTZ,J.S.RICE,B.A.LUXON,J.M.SAYER,G.XIE,H.J.YEH,
JRNL AUTH 2 X.LIU,D.M.JERINA,D.G.GORENSTEIN
JRNL TITL SOLUTION STRUCTURE OF THE MINOR CONFORMER OF A DNA DUPLEX
JRNL TITL 2 CONTAINING A DG MISMATCH OPPOSITE A BENZO[A]PYRENE DIOL
JRNL TITL 3 EPOXIDE/DA ADDUCT: GLYCOSIDIC ROTATION FROM SYN TO ANTI AT
JRNL TITL 4 THE MODIFIED DEOXYADENOSINE.
JRNL REF BIOCHEMISTRY V. 36 11069 1997
JRNL REFN ISSN 0006-2960
JRNL PMID 9333324
JRNL DOI 10.1021/BI971306U
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 4.1
REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,
REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR
REMARK 3 DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1)
REMARK 3 INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM
REMARK 3 RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON
REMARK 3 HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE
REMARK 3 CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF
REMARK 3 THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND
REMARK 3 AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR
REMARK 3 CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE
REMARK 3 MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS
REMARK 3 MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581]
REMARK 3 DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND.
REMARK 3 THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI
REMARK 3 BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH
REMARK 3 THE OPPOSITE DG.
REMARK 3 MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL
REMARK 3 CITATION (SCHWARTZ ET AL.,1997).
REMARK 4
REMARK 4 1BPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB.
REMARK 100 THE DEPOSITION ID IS D_1000008021.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 288
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 76 MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; ROESY; TOCSY; 2D EXCHANGE
REMARK 210 -ONLY SPECTRA
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MORASS 2.2, AMBER 4.1
REMARK 210 METHOD USED : RELAXATION MATRIX REFINEMENT OF
REMARK 210 NOE DISTANCE RESTRAINTS AND
REMARK 210 RESTRAINED MOLECULAR DYNAMICS
REMARK 210 WITH SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED
REMARK 210 USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE
REMARK 210 IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND
REMARK 210 EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT
REMARK 210 ASSIGNMENT PROCESS.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 DC A 4 0.16 SIDE CHAIN
REMARK 500 DA A 5 0.08 SIDE CHAIN
REMARK 500 DG B 13 0.12 SIDE CHAIN
REMARK 500 DA B 16 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BAP A 10
DBREF 1BPS A 1 9 PDB 1BPS 1BPS 1 9
DBREF 1BPS B 10 18 PDB 1BPS 1BPS 10 18
SEQRES 1 A 9 DG DG DT DC DA DC DG DA DG
SEQRES 1 B 9 DC DT DC DG DG DG DA DC DC
HET BAP A 10 38
HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
FORMUL 3 BAP C20 H16 O3
LINK N6 DA A 5 C4' BAP A 10 1555 1555 1.47
SITE 1 AC1 5 DC A 4 DA A 5 DC A 6 DG B 13
SITE 2 AC1 5 DG B 14
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 3 202 Bytes