Header list of 1dl4.pdb file
Complete list - 16 202 Bytes
HEADER DNA 08-DEC-99 1DL4
TITLE THE SOLUTION STRUCTURE OF A BAY-REGION 1S-BENZ[A]ANTHRACENE OXIDE
TITLE 2 ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE
TITLE 3 CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: BENZ[A]ANTHRACENE-MODIFIED ADENINE-6;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3');
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD
KEYWDS BENZ[A]ANTHRACENE-DNA DUPLEX, DNA
EXPDTA SOLUTION NMR
AUTHOR Z.LI,H.-Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS,M.P.STONE
REVDAT 5 16-FEB-22 1DL4 1 REMARK LINK
REVDAT 4 24-FEB-09 1DL4 1 VERSN
REVDAT 3 01-APR-03 1DL4 1 JRNL
REVDAT 2 18-FEB-00 1DL4 1 REMARK HET LINK
REVDAT 1 12-JAN-00 1DL4 0
JRNL AUTH Z.LI,H.Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS,M.P.STONE
JRNL TITL INTERCALATION OF THE
JRNL TITL 2 (1S,2R,3S,4R)-N6-[1-(1,2,3,4-TETRAHYDRO-2,3,
JRNL TITL 3 4-TRIHYDROXYBENZ[A]ANTHRACENYL)]-2'-DEOXYADENOSYL ADDUCT IN
JRNL TITL 4 AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61
JRNL TITL 5 SEQUENCE.
JRNL REF BIOCHEMISTRY V. 38 16045 1999
JRNL REFN ISSN 0006-2960
JRNL PMID 10587427
JRNL DOI 10.1021/BI9903650
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.0, CORMA 5.2
REMARK 3 AUTHORS : BRUKER (XWINNMR), BORGIAS, B.A., THOMAS, P.D., LI,
REMARK 3 H., KUMAR, A., AND TONELLI, M. (CORMA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF
REMARK 3 477 NOE-DERIVED DISTANCE CONSTRAINTS, 80 EMPIRICAL SUGAR PUCKER
REMARK 3 RESTRAINTS, 32 BACKBONE ANGLE DIHEDRAL RESTRAINTS, AND 18
REMARK 3 EMPIRICAL PLANARITY RESTRAINTS.
REMARK 4
REMARK 4 1DL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-99.
REMARK 100 THE DEPOSITION ID IS D_1000010175.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 283; 298
REMARK 210 PH : 7.0; 7.0; 7.0
REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL; 0.1 M
REMARK 210 NACL
REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 1.7 MM OLIGODEOXYNUCLEOTIDE; 10
REMARK 210 MM PHOSPHATE BUFFER; 0.05 MM
REMARK 210 EDTA; 0.1 M NACL; 1.7 MM
REMARK 210 OLIGODEOXYNUCLEOTIDE; 10 MM
REMARK 210 PHOSPHATE BUFFER; 0.05 MM EDTA;
REMARK 210 0.1 M NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D ROESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR 3.851, FELIX 97.0,
REMARK 210 MARDIGRAS 3.0
REMARK 210 METHOD USED : NOE-RESTRAINTED MOLECULAR
REMARK 210 DYNAMICS /SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 7
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.4 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 DA A 6 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 BZA A 12
DBREF 1DL4 A 1 11 PDB 1DL4 1DL4 1 11
DBREF 1DL4 B 12 22 PDB 1DL4 1DL4 12 22
SEQRES 1 A 11 DC DG DG DA DC DA DA DG DA DA DG
SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG
HET BZA A 12 36
HETNAM BZA 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL
FORMUL 3 BZA C18 H16 O3
LINK N6 DA A 6 C4C BZA A 12 1555 1555 1.34
SITE 1 AC1 6 DC A 5 DA A 6 DA A 7 DT B 16
SITE 2 AC1 6 DT B 17 DG B 18
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