Header list of 1dxa.pdb file
Complete list - 16 202 Bytes
HEADER DNA 01-SEP-95 1DXA
TITLE BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3');
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DOUBLE HELIX, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, DUPLEX DNA, NON-
KEYWDS 2 WATSON-CRICK BASE PAIR, DNA
EXPDTA SOLUTION NMR
AUTHOR H.J.C.YEH,J.M.SAYER,X.LIU,A.S.ALTIERI,R.A.BYRD,M.K.LAKSHMAN,H.YAGI,
AUTHOR 2 E.J.SCHURTER,D.G.GORENSTEIN,D.M.JERINA
REVDAT 4 16-FEB-22 1DXA 1 REMARK LINK
REVDAT 3 24-FEB-09 1DXA 1 VERSN
REVDAT 2 01-APR-03 1DXA 1 JRNL
REVDAT 1 07-DEC-95 1DXA 0
JRNL AUTH H.J.YEH,J.M.SAYER,X.LIU,A.S.ALTIERI,R.A.BYRD,M.K.LAKSHMAN,
JRNL AUTH 2 H.YAGI,E.J.SCHURTER,D.G.GORENSTEIN,D.M.JERINA
JRNL TITL NMR SOLUTION STRUCTURE OF A NONANUCLEOTIDE DUPLEX WITH A DG
JRNL TITL 2 MISMATCH OPPOSITE A 10S ADDUCT DERIVED FROM TRANS ADDITION
JRNL TITL 3 OF A DEOXYADENOSINE N6-AMINO GROUP TO
JRNL TITL 4 (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10-
JRNL TITL 5 TETRAHYDROBENZO[A]PYRENE: AN UNUSUAL SYN GLYCOSIDIC TORSION
JRNL TITL 6 ANGLE AT THE MODIFIED DA
JRNL REF BIOCHEMISTRY V. 34 13570 1995
JRNL REFN ISSN 0006-2960
JRNL PMID 7577946
JRNL DOI 10.1021/BI00041A037
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRCHITECT
REMARK 3 AUTHORS : BIOSYM
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: TWO STARTING STRUCTURES WITH
REMARK 3 BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX,
REMARK 3 RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA
REMARK 3 FRAGMENT WITH A MANUALLY BUILD (+)-DE2-[BAP] FRAGMENT. SOLUTION
REMARK 3 STRUCTURES FOR THE DUPLEX WERE GENERATED BY RESTRAINTED
REMARK 3 MOLECULAR DYNAMICS AND RESTRAINTED ENERGY MINIMIZATION USING A
REMARK 3 SET OF INTER-PROTON DISTANCE RESTRAINTS AND DIHEDRAL ANGLE
REMARK 3 RESTRAINTS WHICH WERE DERIVED FROM NMR EXPERIMENTS. SOME OF
REMARK 3 STRUCTURES WITH MINIMUM RESTRAINT VIOLATIONS WERE FURTHER
REMARK 3 REFINED BY THE ITERATIVE RELAXATION MATRIX ANALYSIS (IRMA)
REMARK 3 METHOD OVER 111 WELL-SEPARATED CROSS PEAKS IN NOESY SPECTRA
REMARK 3 RECORDED IN D2O AND MIXING TIMES OF 50, 80, 120, 160 AND 200 MS.
REMARK 3 THE STRUCTURE PRESENTED HERE WAS ONE OF THE FIVE REFINED AND
REMARK 3 MINIMIZED STRUCTURES. THE FOLLOWING RESTRAINTS WERE APPLIED IN
REMARK 3 THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS. THESE
REMARK 3 WERE; (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM
REMARK 3 NOE DATA; (2) BACKBONE DIHEDRAL ANGLE RESTRAINTS FOR A STANDARD
REMARK 3 B-DNA EXCEPT THOSE IMMEDIATELY ADJACENT TO THE MODIFIED RESIDUE;
REMARK 3 (3) DIHEDRAL ANGLE RESTRAINTS FOR ALL GLYCOSIDIC BONDS, EXCEPT
REMARK 3 MODIFIED DA RESIDUE IN THE CENTER; (4) HYDROGEN BOND RESTRAINTS
REMARK 3 (BOTH DISTANCE AND PLANARITY ) FOR ALL BASE-PAIRS EXCEPT CENTRAL
REMARK 3 DA-DG MISMATCH PAIR. THESE RESTRAINTS WERE JUSTIFIED BY THE FACT
REMARK 3 THAT THE MODIFIED DUPLEX DISPLAYED CHARACTERISTIC NMR SPECTRA OF
REMARK 3 A B-DNA EXCEPT NEAR LESION SITE, WHERE THE BAP MOIETY WAS
REMARK 3 INTERCALATED. THE MODIFIED DA RESIDUE DISPLAYED C3'-ENDO SUGAR
REMARK 3 RING AND A SYN GLYCOSIDIC BOND. IT ALSO FORMED A NON-WATSON-
REMARK 3 CRICK BASE PAIR WITH THE OPPOSITE DG.
REMARK 4
REMARK 4 1DXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000172955.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : ENERGY MINIMIZATION, MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10-
REMARK 210 TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC
REMARK 210 N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX
REMARK 210 THROUGH TRANS ADDITION AT THE C10 OF THE EPOXIDE.
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. = 2.5 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DA A 5 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DC B 1 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES
REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.3 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 DG A 2 0.10 SIDE CHAIN
REMARK 500 DT A 3 0.13 SIDE CHAIN
REMARK 500 DA A 5 0.08 SIDE CHAIN
REMARK 500 DA A 8 0.07 SIDE CHAIN
REMARK 500 DT B 2 0.12 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 1DXA A 1 9 PDB 1DXA 1DXA 1 9
DBREF 1DXA B 1 9 PDB 1DXA 1DXA 1 9
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 4 DA A 5 DC A 6 DG B 4 DG B 5
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 - 16 202 Bytes