HEADER DNA 11-JUL-06 2HMR TITLE SOLUTION STRUCTURE OF REDUCED INTERSTRAND CROSS-LINK ARISING FROM S- TITLE 2 ALPHA-METHYL-GAMMA-OH-1,N2-PROPANO-2'-DEOXYGUANOSINE IN THE 5'-CPG-3' TITLE 3 DNA SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DODECAMER WITH INTERSTRAND CROSS-LINK; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: G7 OF CHAIN A AND B LINKED; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA DODECAMER WITH INTERSTRAND CROSS-LINK; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: G7 OF CHAIN A AND B LINKED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS CROTONALDEHYDE INTERSTRAND DNA CROSS-LINK, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR Y.-J.CHO,I.D.KOZEKOV,T.M.HARRIS,C.J.RIZZO,M.P.STONE REVDAT 4 09-MAR-22 2HMR 1 REMARK LINK REVDAT 3 24-FEB-09 2HMR 1 VERSN REVDAT 2 10-APR-07 2HMR 1 JRNL REVDAT 1 13-MAR-07 2HMR 0 JRNL AUTH Y.-J.CHO,I.D.KOZEKOV,T.M.HARRIS,C.J.RIZZO,M.P.STONE JRNL TITL STEREOCHEMISTRY MODULATES THE STABILITY OF REDUCED JRNL TITL 2 INTERSTRAND CROSS-LINKS ARISING FROM R- AND JRNL TITL 3 S-ALPHA-CH(3)-GAMMA-OH-1,N(2)-PROPANO-2'-DEOXYGUANOSINE IN JRNL TITL 4 THE 5'-CPG-3' DNA SEQUENCE JRNL REF BIOCHEMISTRY V. 46 2608 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17305317 JRNL DOI 10.1021/BI061381H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 8.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), CASE ET AL (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HMR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038523. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 286 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1M NACL; 0.1M NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM IN 0.25 ML; 10 MM NAH2PO4; REMARK 210 0.1 M NACL; 50 UM NA2EDTA; 2MM REMARK 210 IN 0.25 ML; 10 MM NAH2PO4; 0.1 M REMARK 210 NACL; 50 UM NA2EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, FELIX 2000, REMARK 210 MARDIGRAS 5.2.1, CORMA 5.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 2 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 10 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 14 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC B 16 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 20 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 22 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 23 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 23 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC A 6 0.08 SIDE CHAIN REMARK 500 DG B 13 0.07 SIDE CHAIN REMARK 500 DG B 14 0.09 SIDE CHAIN REMARK 500 DC B 18 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HLI RELATED DB: PDB REMARK 900 S-METHYL STEREOCHEMISTRY BUT OPENED SPECIES (CROSS-LINK PRECURSOR) REMARK 900 RELATED ID: 2HMD RELATED DB: PDB REMARK 900 R-METHYL STEREOCHEMISTRY DBREF 2HMR A 1 12 PDB 2HMR 2HMR 1 12 DBREF 2HMR B 13 24 PDB 2HMR 2HMR 13 24 SEQRES 1 A 12 DG DC DT DA DG DC 2EG DA DG DT DC DC SEQRES 1 B 12 DG DG DA DC DT DC 2EG DC DT DA DG DC MODRES 2HMR 2EG A 7 G 2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE MODRES 2HMR 2EG B 19 G 2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE HET 2EG A 7 38 HET 2EG B 19 38 HETNAM 2EG 2'-DEOXY-N-ETHYLGUANOSINE 5'-PHOSPHATE FORMUL 1 2EG 2(C12 H18 N5 O7 P) LINK O3' DC A 6 P 2EG A 7 1555 1555 1.61 LINK O3' 2EG A 7 P DA A 8 1555 1555 1.61 LINK C21 2EG A 7 C22 2EG B 19 1555 1555 1.56 LINK O3' DC B 18 P 2EG B 19 1555 1555 1.61 LINK O3' 2EG B 19 P DC B 20 1555 1555 1.61 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