HEADER DNA 19-JAN-99 1B6X TITLE 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE GUANINE IN AN 11-MER DUPLEX, TITLE 2 SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 4 STRUCTURES CAVEAT 1B6X THERE IS A CHIRALITY ERROR AT ATOM C1' OF EDC A 6 IN MODEL CAVEAT 2 1B6X 1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, ETHENODC, EDC, EXOCYCLIC LESION, DNA EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR D.CULLINAN,F.JOHNSON,A.P.GROLLMAN,M.EISENBERG,C.DE LOS SANTOS REVDAT 6 10-APR-24 1B6X 1 REMARK LINK REVDAT 5 18-JAN-12 1B6X 1 HETATM HETSYN FORMUL REMARK REVDAT 4 24-FEB-09 1B6X 1 VERSN REVDAT 3 01-APR-03 1B6X 1 JRNL REVDAT 2 06-APR-99 1B6X 1 HET COMPND REMARK TITLE REVDAT 2 2 1 HETATM SEQADV EXPDTA HEADER REVDAT 2 3 1 MODRES LINK SOURCE AUTHOR REVDAT 2 4 1 SEQRES FORMUL JRNL KEYWDS REVDAT 2 5 1 HETSYN CONECT REVDAT 1 27-JAN-99 1B6X 0 JRNL AUTH D.CULLINAN,F.JOHNSON,A.P.GROLLMAN,M.EISENBERG, JRNL AUTH 2 C.DE LOS SANTOS JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE EXOCYCLIC JRNL TITL 2 LESION 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE JRNL TITL 3 2'-DEOXYGUANOSINE. JRNL REF BIOCHEMISTRY V. 36 11933 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9305987 JRNL DOI 10.1021/BI9705725 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: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1B6X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171506. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 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; TOCSY; REMARK 210 COSY45; 15N-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AM; AND AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER 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 : 4 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR FOLLOWED REMARK 210 BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND REMARK 210 FURTHER REFINED USING THE FULL RELAXATION MATRIX BACK REMARK 210 CALCULATION APPROACH. 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 1 DC A 1 C4 DC A 1 N4 0.095 REMARK 500 1 DG A 2 C2 DG A 2 N2 0.081 REMARK 500 1 DT A 3 C5 DT A 3 C7 0.036 REMARK 500 1 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 1 DC A 5 C4 DC A 5 N4 0.094 REMARK 500 1 DC A 7 C4 DC A 7 N4 0.096 REMARK 500 1 DA A 8 C6 DA A 8 N6 0.094 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 1 DG A 10 C2 DG A 10 N2 0.083 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.097 REMARK 500 1 DG B 1 C2 DG B 1 N2 0.078 REMARK 500 1 DC B 2 C4 DC B 2 N4 0.093 REMARK 500 1 DA B 3 C6 DA B 3 N6 0.093 REMARK 500 1 DG B 5 C2 DG B 5 N2 0.080 REMARK 500 1 DG B 6 C2 DG B 6 N2 0.077 REMARK 500 1 DG B 7 C2 DG B 7 N2 0.084 REMARK 500 1 DT B 8 C5 DT B 8 C7 0.036 REMARK 500 1 DA B 9 C6 DA B 9 N6 0.095 REMARK 500 1 DC B 10 C4 DC B 10 N4 0.096 REMARK 500 1 DG B 11 C2 DG B 11 N2 0.084 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.096 REMARK 500 2 DG A 2 C2 DG A 2 N2 0.080 REMARK 500 2 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 2 DC A 5 C4 DC A 5 N4 0.096 REMARK 500 2 DC A 7 C4 DC A 7 N4 0.094 REMARK 500 2 DA A 8 C6 DA A 8 N6 0.094 REMARK 500 2 DG A 10 C2 DG A 10 N2 0.083 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.096 REMARK 500 2 DG B 1 C2 DG B 1 N2 0.078 REMARK 500 2 DC B 2 C4 DC B 2 N4 0.093 REMARK 500 2 DA B 3 C6 DA B 3 N6 0.092 REMARK 500 2 DG B 5 C2 DG B 5 N2 0.082 REMARK 500 2 DG B 6 C2 DG B 6 N2 0.083 REMARK 500 2 DG B 7 C2 DG B 7 N2 0.083 REMARK 500 2 DT B 8 C5 DT B 8 C7 0.037 REMARK 500 2 DA B 9 C6 DA B 9 N6 0.095 REMARK 500 2 DC B 10 C4 DC B 10 N4 0.095 REMARK 500 2 DG B 11 C2 DG B 11 N2 0.084 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.095 REMARK 500 3 DG A 2 C2 DG A 2 N2 0.081 REMARK 500 3 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 3 DC A 5 C4 DC A 5 N4 0.094 REMARK 500 3 DC A 7 C4 DC A 7 N4 0.093 REMARK 500 3 DA A 8 C6 DA A 8 N6 0.094 REMARK 500 3 DG A 10 C2 DG A 10 N2 0.083 REMARK 500 3 DC A 11 C4 DC A 11 N4 0.096 REMARK 500 3 DG B 1 C2 DG B 1 N2 0.078 REMARK 500 3 DC B 2 C4 DC B 2 N4 0.094 REMARK 500 3 DA B 3 C6 DA B 3 N6 0.093 REMARK 500 3 DG B 5 C2 DG B 5 N2 0.082 REMARK 500 REMARK 500 THIS ENTRY HAS 75 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 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG B 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 3 DG B 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DC A 5 C3' - O3' - P ANGL. DEV. = 11.0 DEGREES REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 4 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1B6X A 1 11 PDB 1B6X 1B6X 1 11 DBREF 1B6X B 1 11 PDB 1B6X 1B6X 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 DG 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 MODEL 1