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 5 27-DEC-23 1B60 1 REMARK LINK 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 DEPOSITION ID IS D_1000007019. 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: REMARK 210 SEE DETAILS. THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR REMARK 210 FOLLOWED BY REMARK 210 DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REMARK 210 REFINED USING REMARK 210 THE FULL RELAXATION MATRIX BACK CALCULATION APPROACH. 15 REMARK 210 STRUCTURES EACH WERE REMARK 210 DETERMINED FROM A- AND B-FORM DNA BY USING DIFFERENT INITIAL REMARK 210 TEMPERATURES AND REMARK 210 DIFFERENT LENGTHS OF TIME AT THE HIGH TEMPERATURE STAGE OF THE 30 REMARK 210 STRUCTURES REMARK 210 FROM DISTANCE RESTRAINED DYNAMICS, 27 HAD AN RMSD TO THEIR AVERAGE REMARK 210 OF LESS REMARK 210 THAN 0.4 A, SO THE AVERAGE OF THESE 27 WAS USED AS THE STARTING REMARK 210 STRUCTURE FOR REMARK 210 FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE REMARK 210 STRUCTURE FROM REMARK 210 THIS LAST 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. = -5.2 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. = 2.1 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 O3' DC A 5 P EDC A 6 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