Header list of 1b60.pdb file
Complete list - 25 201 Bytes
HEADER DNA 20-JAN-99 1B60
TITLE 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX,
TITLE 2 SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ETHENODC, EDC, EPSILON-DC;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3');
COMPND 8 CHAIN: B;
COMPND 9 SYNONYM: ETHENODC, EDC, EPSILON-DC;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS ETHENODC, EDC, EXOCYCLIC LESION, DNA
EXPDTA SOLUTION NMR
AUTHOR D.CULLINAN,F.JOHNSON,C.DE LOS SANTOS
REVDAT 4 18-JAN-12 1B60 1 VERSN HETATM HETSYN FORMUL
REVDAT 4 2 1 REMARK
REVDAT 3 24-FEB-09 1B60 1 VERSN
REVDAT 2 01-APR-03 1B60 1 JRNL
REVDAT 1 18-FEB-00 1B60 0
JRNL AUTH D.CULLINAN,F.JOHNSON,C.DE LOS SANTOS
JRNL TITL SOLUTION STRUCTURE OF AN 11-MER DUPLEX CONTAINING THE 3,
JRNL TITL 2 N(4)-ETHENOCYTOSINE ADDUCT OPPOSITE 2'-DEOXYCYTIDINE:
JRNL TITL 3 IMPLICATIONS FOR THE RECOGNITION OF EXOCYCLIC LESIONS BY DNA
JRNL TITL 4 GLYCOSYLASES.
JRNL REF J.MOL.BIOL. V. 296 851 2000
JRNL REFN ISSN 0022-2836
JRNL PMID 10677286
JRNL DOI 10.1006/JMBI.1999.3490
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE EXOCYCLIC
REMARK 1 TITL 2 LESION 3,N4-ETHENO- 2'-DEOXYCYTIDINE OPPOSITE
REMARK 1 TITL 3 2'-DEOXYGUANOSINE
REMARK 1 REF BIOCHEMISTRY V. 36 11933 1997
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 1B60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-99.
REMARK 100 THE RCSB ID CODE IS RCSB007019.
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 : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; DQF-COSY; COSY45;
REMARK 210 TOCSY; HETCORR
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX, X-PLOR
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210 SIMULATIONS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : SEE DETAILS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: SEE DETAILS. THE STRUCTURE WAS DETERMINED USING 2D PROTON
REMARK 210 NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS
REMARK 210 SIMULATIONS, AND FURTHER REFINED USING THE FULL RELAXATION MATRIX
REMARK 210 BACK CALCULATION APPROACH. 15 STRUCTURES EACH WERE DETERMINED
REMARK 210 FROM A- AND B-FORM DNA BY USING DIFFERENT INITIAL TEMPERATURES
REMARK 210 AND DIFFERENT LENGTHS OF TIME AT THE HIGH TEMPERATURE STAGE OF
REMARK 210 THE 30 STRUCTURES FROM DISTANCE RESTRAINED DYNAMICS, 27 HAD AN
REMARK 210 RMSD TO THEIR AVERAGE OF LESS THAN 0.4 A, SO THE AVERAGE OF THESE
REMARK 210 27 WAS USED AS THE STARTING STRUCTURE FOR FULL RELAXATION MATRIX
REMARK 210 BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST
REMARK 210 STEP IS WHAT HAS BEEN DEPOSITED.
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 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 DC A 1 C4 DC A 1 N4 0.094
REMARK 500 DG A 2 C2 DG A 2 N2 0.080
REMARK 500 DA A 4 C6 DA A 4 N6 0.093
REMARK 500 DC A 5 C4 DC A 5 N4 0.095
REMARK 500 DC A 7 C4 DC A 7 N4 0.094
REMARK 500 DA A 8 C6 DA A 8 N6 0.093
REMARK 500 DG A 10 C2 DG A 10 N2 0.083
REMARK 500 DC A 11 C4 DC A 11 N4 0.095
REMARK 500 DG B 1 C2 DG B 1 N2 0.079
REMARK 500 DC B 2 C4 DC B 2 N4 0.095
REMARK 500 DA B 3 C6 DA B 3 N6 0.093
REMARK 500 DG B 5 C2 DG B 5 N2 0.082
REMARK 500 DC B 6 C4 DC B 6 N4 0.088
REMARK 500 DG B 7 C2 DG B 7 N2 0.082
REMARK 500 DT B 8 C5 DT B 8 C7 0.036
REMARK 500 DA B 9 C6 DA B 9 N6 0.093
REMARK 500 DC B 10 C4 DC B 10 N4 0.095
REMARK 500 DG B 11 C2 DG B 11 N2 0.084
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. = 2.4 DEGREES
REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES
REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DG B 7 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1B60 A 1 11 PDB 1B60 1B60 1 11
DBREF 1B60 B 1 11 PDB 1B60 1B60 1 11
SEQRES 1 A 11 DC DG DT DA DC EDC DC DA DT DG DC
SEQRES 1 B 11 DG DC DA DT DG DC DG DT DA DC DG
HET EDC A 6 32
HETNAM EDC N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
HETSYN EDC 6-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-
HETSYN 2 EDC PENTOFURANOSYL)IMIDAZO[1,2-C]PYRIMIDIN-5(6H)-ONE
FORMUL 1 EDC C11 H14 N3 O7 P
LINK P EDC A 6 O3' DC A 5 1555 1555 1.62
LINK O3' EDC A 6 P DC A 7 1555 1555 1.62
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 - 25 201 Bytes