Header list of 1hx4.pdb file
Complete list - 23 20 Bytes
HEADER DNA 11-JAN-01 1HX4
TITLE MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA
TITLE 2 ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHESIZED FROM ABI-DNA SYNTHESIZER;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: SYNTHESIZED FROM ABI-DNA SYNTHESIZER
KEYWDS 1R-TRANS-ANTI-BPH-N2-G ADDUCT, CARCINOGEN-DNA ADDUCT,
KEYWDS 2 BENZO[C]PHENANTHRENE DNA ADDUCT, DNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR D.J.PATEL,C.H.LIN,N.E.GEACINTOV,S.BROYDE,X.HUANG,A.KOLBANOVSKII,
AUTHOR 2 B.E.HINGERTY,S.AMIN
REVDAT 3 23-FEB-22 1HX4 1 REMARK LINK
REVDAT 2 24-FEB-09 1HX4 1 VERSN
REVDAT 1 21-MAR-01 1HX4 0
JRNL AUTH C.H.LIN,X.HUANG,A.KOLBANOVSKII,B.E.HINGERTY,S.AMIN,S.BROYDE,
JRNL AUTH 2 N.E.GEACINTOV,D.J.PATEL
JRNL TITL MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS
JRNL TITL 2 DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC
JRNL TITL 3 ACTIVITY.
JRNL REF J.MOL.BIOL. V. 306 1059 2001
JRNL REFN ISSN 0022-2836
JRNL PMID 11237618
JRNL DOI 10.1006/JMBI.2001.4425
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1, X-PLOR 3.1
REMARK 3 AUTHORS : VARIAN ASSOCIATES INC. (VNMR), BRUNGER, A. T. (X
REMARK 3 -PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NONEXCHANGEABLE INTERPROTON DISTANCE
REMARK 3 RESTRAINTS WERE OBTAINED FROM THE BUILDUP OF NOE CROSS PEAK
REMARK 3 VOLUMES IN NOESY DATA SETS (55, 100, 150 AND 200 MS MIXING TIMES)
REMARK 3 ON THE 1S-(-)-TRANS-ANTI-(BPH)G*C AND THE 1R-(+)-TRANS-ANTI-
REMARK 3 (BPH)G*C 11-MER DNA DUPLEX ADDUCTS IN D2O BUFFER AT 23 AND 18 SC,
REMARK 3 RESPECTIVELY, AND BOUNDS WERE SET BETWEEN 15% AND 25% OF THE
REMARK 3 CALCULATED DISTANCES USING THE FIXED CYTIDINE H5-H6 REFERENCE
REMARK 3 DISTANCE OF 2.45 . NON-STEREOSPECIFIC ASSIGNMENTS WERE TREATED
REMARK 3 WITH R-6 AVERAGING. INTERPROTON DISTANCE RESTRAINTS INVOLVING
REMARK 3 EXCHANGEABLE PROTONS OF THE SAME COMPLEX WERE OBTAINED FROM
REMARK 3 NOESY SPECTRA (90 AND 150 MS MIXING TIMES) IN H2O BUFFER AT 4 SC
REMARK 3 WITH BOUNDS SET BETWEEN 20% AND 25% OF THE CALCULATED DISTANCE
REMARK 3 USING THE THYMINE IMINO TO ADENINE H2 REFERENCE DISTANCE OF 2.91
REMARK 3 ACROSS AN A*T BASE PAIR.
REMARK 4
REMARK 4 1HX4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-01.
REMARK 100 THE DEPOSITION ID IS D_1000012648.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 277
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 0.10
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 1R-TRANS-ANTI-BPH (CARCINOGEN)
REMARK 210 COVALENTLY BOUND TO 11MER DNA
REMARK 210 DUPLEX
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; P-COSY; 1H-31P HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 400 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX FELIX2000
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING, RELAXATION
REMARK 210 MATRIX REFINEMENTS, ENERGE
REMARK 210 MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 9
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9
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: D2O NMR EXPERIMENTS WERE PERFORMED AT 13 DEGREE C, H2O NMR
REMARK 210 EXPERIMENTS WERE PERFORMED AT 4 DEGREE C
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 1 DC A 2 N1 DC A 2 C6 -0.038
REMARK 500 1 DG A 6 N7 DG A 6 C8 0.045
REMARK 500 1 DA A 9 C3' DA A 9 C2' -0.059
REMARK 500 1 DG B 12 N7 DG B 12 C8 0.041
REMARK 500 1 DG B 13 N7 DG B 13 C8 0.050
REMARK 500 1 DA B 15 N7 DA B 15 C8 0.043
REMARK 500 1 DG B 16 N7 DG B 16 C8 0.045
REMARK 500 1 DG B 18 N7 DG B 18 C8 0.040
REMARK 500 1 DG B 21 N7 DG B 21 C8 0.045
REMARK 500 1 DG B 22 N7 DG B 22 C8 0.045
REMARK 500 2 DC A 2 N1 DC A 2 C6 -0.037
REMARK 500 2 DG A 6 N7 DG A 6 C8 0.046
REMARK 500 2 DT A 8 C6 DT A 8 N1 -0.043
REMARK 500 2 DA A 9 C3' DA A 9 C2' -0.057
REMARK 500 2 DG B 12 N7 DG B 12 C8 0.046
REMARK 500 2 DG B 13 C3' DG B 13 C2' -0.049
REMARK 500 2 DG B 13 N7 DG B 13 C8 0.046
REMARK 500 2 DT B 14 C6 DT B 14 N1 -0.043
REMARK 500 2 DG B 16 N7 DG B 16 C8 0.043
REMARK 500 2 DG B 18 N7 DG B 18 C8 0.043
REMARK 500 2 DG B 21 N7 DG B 21 C8 0.048
REMARK 500 2 DG B 22 N7 DG B 22 C8 0.046
REMARK 500 3 DC A 2 N1 DC A 2 C6 -0.038
REMARK 500 3 DG A 6 N7 DG A 6 C8 0.047
REMARK 500 3 DT A 8 C6 DT A 8 N1 -0.042
REMARK 500 3 DA A 9 C3' DA A 9 C2' -0.059
REMARK 500 3 DG B 12 N7 DG B 12 C8 0.047
REMARK 500 3 DG B 13 N7 DG B 13 C8 0.049
REMARK 500 3 DT B 14 C6 DT B 14 N1 -0.043
REMARK 500 3 DG B 16 N7 DG B 16 C8 0.042
REMARK 500 3 DG B 18 N7 DG B 18 C8 0.042
REMARK 500 3 DG B 21 N7 DG B 21 C8 0.048
REMARK 500 3 DG B 22 N7 DG B 22 C8 0.042
REMARK 500 4 DC A 2 N1 DC A 2 C6 -0.039
REMARK 500 4 DG A 6 N7 DG A 6 C8 0.048
REMARK 500 4 DA A 9 C3' DA A 9 C2' -0.057
REMARK 500 4 DG B 12 N7 DG B 12 C8 0.048
REMARK 500 4 DG B 13 N7 DG B 13 C8 0.051
REMARK 500 4 DT B 14 C6 DT B 14 N1 -0.043
REMARK 500 4 DG B 16 N7 DG B 16 C8 0.042
REMARK 500 4 DG B 18 N7 DG B 18 C8 0.041
REMARK 500 4 DG B 21 N7 DG B 21 C8 0.046
REMARK 500 4 DG B 22 N7 DG B 22 C8 0.045
REMARK 500 5 DC A 2 N1 DC A 2 C6 -0.038
REMARK 500 5 DG A 6 N7 DG A 6 C8 0.047
REMARK 500 5 DA A 9 C3' DA A 9 C2' -0.059
REMARK 500 5 DG B 12 N7 DG B 12 C8 0.044
REMARK 500 5 DG B 13 C3' DG B 13 C2' -0.064
REMARK 500 5 DG B 13 N7 DG B 13 C8 0.049
REMARK 500 5 DG B 16 N7 DG B 16 C8 0.041
REMARK 500
REMARK 500 THIS ENTRY HAS 95 BOND DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
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 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 DC A 5 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DG A 6 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 DC A 7 N1 - C1' - C2' ANGL. DEV. = 9.9 DEGREES
REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT A 8 C4 - C5 - C7 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 DT A 8 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES
REMARK 500 1 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG B 13 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DT B 14 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 1 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DT B 14 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DT B 14 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 DT B 14 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES
REMARK 500 1 DG B 16 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DC B 17 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DC B 17 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DG B 18 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 DT B 20 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DT B 20 C4 - C5 - C7 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 DG B 21 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DC A 2 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 2 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DT A 4 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES
REMARK 500 2 DG A 6 C1' - O4' - C4' ANGL. DEV. = -8.5 DEGREES
REMARK 500 2 DG A 6 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 2 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DC A 7 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES
REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 DT A 8 C4 - C5 - C7 ANGL. DEV. = 6.2 DEGREES
REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -7.5 DEGREES
REMARK 500 2 DT A 8 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 314 ANGLE DEVIATIONS.
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 BPJ A 25
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HWV RELATED DB: PDB
REMARK 900 1S-TRANS-ANTI-(BPH)-N2-DG ADDUCT, CARCINOGEN-DNA ADDUCT
DBREF 1HX4 A 1 11 PDB 1HX4 1HX4 1 11
DBREF 1HX4 B 12 22 PDB 1HX4 1HX4 12 22
SEQRES 1 A 11 DC DC DA DT DC DG DC DT DA DC DC
SEQRES 1 B 11 DG DG DT DA DG DC DG DA DT DG DG
HET BPJ A 25 36
HETNAM BPJ (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-
HETNAM 2 BPJ TRIOL
HETSYN BPJ 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE
FORMUL 3 BPJ C18 H16 O3
LINK N2 DG A 6 C1 BPJ A 25 1555 1555 1.34
SITE 1 AC1 6 DG A 6 DC A 7 DG B 16 DC B 17
SITE 2 AC1 6 DG B 18 DA B 19
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
MODEL 1
Complete list - 23 20 Bytes