Header list of 1qkg.pdb file
Complete list - 9 202 Bytes
HEADER DNA 20-JUL-99 1QKG
TITLE DNA DECAMER DUPLEX CONTAINING T-T DEWAR PHOTOPRODUCT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*(HYD)TP*+TP*AP*CP*GP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: BOND FORMED BETWEEN C6(T5) AND C4(T6) BOND FORMED
COMPND 6 BETWEEN N3(T6) AND C6(T6);
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3');
COMPND 9 CHAIN: B;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DEOXYRIBONUCLEIC ACID, DNA PHOTOPRODUCT, DEWAR PRODUCT, (6-4) ADDUCT,
KEYWDS 2 MUTAGENESIS, TRANSLESION REPLICATION, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR J.-H.LEE,S.-H.BAE,Y.-J.CHOI,B.-S.CHOI
REVDAT 8 14-JUN-23 1QKG 1 REMARK
REVDAT 7 15-JAN-20 1QKG 1 LINK
REVDAT 6 02-FEB-10 1QKG 1 KEYWDS REMARK HETATM ATOM
REVDAT 6 2 1 TER CONECT MASTER
REVDAT 5 02-JUN-09 1QKG 1 FORMUL
REVDAT 4 24-FEB-09 1QKG 1 VERSN
REVDAT 3 14-JUN-06 1QKG 1 ATOM
REVDAT 2 24-MAY-00 1QKG 1 JRNL
REVDAT 1 11-MAY-00 1QKG 0
JRNL AUTH J.-H.LEE,S.-H.BAE,B.-S.CHOI
JRNL TITL THE DEWAR PHOTOPRODUCT OF THYMIDYLYL(3'-->5')-THYMIDINE
JRNL TITL 2 (DEWAR PRODUCT) EXHIBITS MUTAGENIC BEHAVIOR IN ACCORDANCE
JRNL TITL 3 WITH THE "A RULE".
JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 4591 2000
JRNL REFN ISSN 0027-8424
JRNL PMID 10758155
JRNL DOI 10.1073/PNAS.080057097
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS WITH NMR
REMARK 3 -DERIVEN DISTANCE RESTRAINTS AND THEN FULL RELAXATION MATRIX
REMARK 3 REFINEMENT WITH NOE VOLUME ITENSITY RESTRAINTS
REMARK 4
REMARK 4 1QKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUL-99.
REMARK 100 THE DEPOSITION ID IS D_1290002961.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 274.0
REMARK 210 PH : 6.6
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : 100% D2O, 10% WATER/90% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : SIMULATED ANNEALING AND FULL
REMARK 210 RELAXATION MATRIX REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 8
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING SA
REMARK 210 METHOD WITH DISTANCE RESTRAINTS AND FULL RELAXATION MATRIX
REMARK 210 REFINEMENT WITH NOE INTENSITY RESTRAINTS OF 50, 80, 160 MS
REMARK 210 MIXING TIMES
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1890 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3760 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL
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 400
REMARK 400 COMPOUND
REMARK 400 MISMATCHED BASE PAIRING OF 3'-T OF DEWAR PRODUCT WITH G RESIDUE
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 DA A 4 N9 DA A 4 C4 0.039
REMARK 500 DT B 17 N1 DT B 17 C2 0.053
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 12.6 DEGREES
REMARK 500 DC A 3 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DC A 3 C3' - O3' - P ANGL. DEV. = 21.5 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DA A 4 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 64T A 5 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 TA3 A 6 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 DA A 7 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES
REMARK 500 DC A 8 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DC A 8 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES
REMARK 500 DG A 9 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG A 9 C3' - O3' - P ANGL. DEV. = 16.5 DEGREES
REMARK 500 DG B 11 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES
REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG B 11 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG B 11 C3' - O3' - P ANGL. DEV. = 17.0 DEGREES
REMARK 500 DC B 12 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES
REMARK 500 DG B 13 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG B 13 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES
REMARK 500 DT B 14 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES
REMARK 500 DG B 15 N3 - C2 - N2 ANGL. DEV. = 7.4 DEGREES
REMARK 500 DG B 15 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 DA B 16 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES
REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 DA B 16 C3' - O3' - P ANGL. DEV. = 15.7 DEGREES
REMARK 500 DT B 17 C3' - O3' - P ANGL. DEV. = 18.4 DEGREES
REMARK 500 DG B 18 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 18 C3' - O3' - P ANGL. DEV. = 17.6 DEGREES
REMARK 500 DC B 19 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CFL RELATED DB: PDB
REMARK 900 DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT
REMARK 900 RELATED ID: 4409 RELATED DB: BMRB
DBREF 1QKG A 1 10 PDB 1QKG 1QKG 1 10
DBREF 1QKG B 11 20 PDB 1QKG 1QKG 11 20
SEQRES 1 A 10 DC DG DC DA 64T TA3 DA DC DG DC
SEQRES 1 B 10 DG DC DG DT DG DA DT DG DC DG
MODRES 1QKG 64T A 5 DT 5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE
MODRES 1QKG TA3 A 6 DT
HET 64T A 5 34
HET TA3 A 6 30
HETNAM 64T 5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE
HETNAM TA3 (4S,5R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-
HETNAM 2 TA3 PENTOFURANOSYL)-5-METHYL-1,3-DIAZABICYCLO[2.2.0]HEXAN-
HETNAM 3 TA3 2-ONE
FORMUL 1 64T C10 H17 N2 O9 P
FORMUL 1 TA3 C10 H17 N2 O7 P
LINK O3' DA A 4 P 64T A 5 1555 1555 1.61
LINK O3' 64T A 5 P TA3 A 6 1555 1555 1.61
LINK C6 64T A 5 C4 TA3 A 6 1555 1555 1.50
LINK O3' TA3 A 6 P DA A 7 1555 1555 1.60
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 - 9 202 Bytes