HEADER DNA 28-FEB-03 1ONM TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A:G MISMATCH. TITLE 2 D(GCTTCAGTCGT):D(ACGACGGAAGC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*TP*TP*CP*AP*GP*TP*CP*GP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*CP*GP*AP*CP*GP*GP*AP*AP*GP*C)-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 A/G MISMATCH, A:G MISMATCH, A/G MISPAIR, A:G MISPAIR, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.M.SANCHEZ,D.E.VOLK,D.G.GORENSTEIN,R.S.LLOYD REVDAT 3 23-FEB-22 1ONM 1 REMARK REVDAT 2 24-FEB-09 1ONM 1 VERSN REVDAT 1 04-NOV-03 1ONM 0 JRNL AUTH A.M.SANCHEZ,D.E.VOLK,D.G.GORENSTEIN,R.S.LLOYD JRNL TITL INITIATION OF REPAIR OF A/G MISMATCHES IS MODULATED BY JRNL TITL 2 SEQUENCE CONTEXT JRNL REF DNA REPAIR V. 2 863 2003 JRNL REFN ISSN 1568-7864 JRNL PMID 12893083 JRNL DOI 10.1016/S1568-7864(03)00067-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, AMBER 5 REMARK 3 AUTHORS : VARIAN, INC. (VNMR), CASE, D.A. ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 624 TOTAL RESTRAINTS WERE USED: 500 REMARK 3 DERIVED FROM 2D NOE DATA AND 124 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1ONM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018476. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 288 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 25 MM PHOSPHATE,50 MM NACL; 25 REMARK 210 MM PHOSPHATE,50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA DUPLEX; 25 MM REMARK 210 PHOSPHATE, 50 MM NACL, 1 MM EDTA; REMARK 210 ; 1 MM DNA DUPLEX; 25 MM REMARK 210 PHOSPHATE, 50 MM NACL, 1 MM EDTA; REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.51 REMARK 210 METHOD USED : TOTAL RELAXATION MATRIX AND REMARK 210 MOLECULAR DYNAMICS WERE USED. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 DA B 20 C5' DA B 20 C4' 0.043 REMARK 500 2 DG A 7 C5' DG A 7 C4' 0.042 REMARK 500 2 DA B 19 C5' DA B 19 C4' 0.043 REMARK 500 5 DA B 20 C5' DA B 20 C4' 0.044 REMARK 500 6 DC A 2 C5' DC A 2 C4' 0.043 REMARK 500 7 DC B 13 C5' DC B 13 C4' 0.043 REMARK 500 7 DG B 18 C5' DG B 18 C4' 0.046 REMARK 500 8 DC A 5 C5' DC A 5 C4' 0.043 REMARK 500 8 DG A 10 C5' DG A 10 C4' 0.042 REMARK 500 9 DG B 17 C5' DG B 17 C4' 0.047 REMARK 500 10 DC A 2 C5' DC A 2 C4' 0.044 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 10 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 11 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 12 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 12 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 12 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DC B 16 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 16 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG B 18 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA B 20 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 20 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 20 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC B 22 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 22 N3 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 22 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 5 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DC A 5 N3 - C4 - N4 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DA A 6 C4 - C5 - C6 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DA A 6 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 DG A 7 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 8 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 352 ANGLE DEVIATIONS. 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 1 DC A 2 0.07 SIDE CHAIN REMARK 500 1 DT A 4 0.08 SIDE CHAIN REMARK 500 1 DG A 7 0.06 SIDE CHAIN REMARK 500 1 DA B 12 0.06 SIDE CHAIN REMARK 500 1 DG B 14 0.07 SIDE CHAIN REMARK 500 2 DA A 6 0.06 SIDE CHAIN REMARK 500 2 DT A 11 0.08 SIDE CHAIN REMARK 500 2 DA B 12 0.09 SIDE CHAIN REMARK 500 2 DC B 13 0.08 SIDE CHAIN REMARK 500 2 DG B 17 0.12 SIDE CHAIN REMARK 500 3 DG A 1 0.10 SIDE CHAIN REMARK 500 3 DC A 9 0.07 SIDE CHAIN REMARK 500 3 DT A 11 0.07 SIDE CHAIN REMARK 500 3 DG B 14 0.07 SIDE CHAIN REMARK 500 3 DC B 22 0.07 SIDE CHAIN REMARK 500 4 DG A 1 0.10 SIDE CHAIN REMARK 500 4 DC A 5 0.07 SIDE CHAIN REMARK 500 4 DT A 8 0.07 SIDE CHAIN REMARK 500 4 DA B 12 0.10 SIDE CHAIN REMARK 500 4 DG B 14 0.06 SIDE CHAIN REMARK 500 4 DG B 21 0.07 SIDE CHAIN REMARK 500 5 DT A 4 0.08 SIDE CHAIN REMARK 500 5 DG B 14 0.06 SIDE CHAIN REMARK 500 5 DG B 17 0.06 SIDE CHAIN REMARK 500 5 DG B 21 0.07 SIDE CHAIN REMARK 500 5 DC B 22 0.07 SIDE CHAIN REMARK 500 6 DC A 5 0.09 SIDE CHAIN REMARK 500 6 DG A 10 0.07 SIDE CHAIN REMARK 500 6 DC B 13 0.08 SIDE CHAIN REMARK 500 6 DG B 14 0.10 SIDE CHAIN REMARK 500 6 DC B 22 0.08 SIDE CHAIN REMARK 500 7 DG A 1 0.07 SIDE CHAIN REMARK 500 7 DG A 7 0.07 SIDE CHAIN REMARK 500 7 DG A 10 0.07 SIDE CHAIN REMARK 500 7 DA B 12 0.06 SIDE CHAIN REMARK 500 7 DG B 17 0.09 SIDE CHAIN REMARK 500 8 DG A 1 0.07 SIDE CHAIN REMARK 500 8 DC B 16 0.07 SIDE CHAIN REMARK 500 8 DG B 18 0.06 SIDE CHAIN REMARK 500 9 DC A 2 0.09 SIDE CHAIN REMARK 500 9 DT A 4 0.08 SIDE CHAIN REMARK 500 9 DG A 7 0.06 SIDE CHAIN REMARK 500 9 DC B 22 0.06 SIDE CHAIN REMARK 500 10 DG A 1 0.09 SIDE CHAIN REMARK 500 10 DT A 11 0.09 SIDE CHAIN REMARK 500 10 DG B 14 0.12 SIDE CHAIN REMARK 500 10 DG B 17 0.07 SIDE CHAIN REMARK 500 10 DG B 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1ONM A 1 11 PDB 1ONM 1ONM 1 11 DBREF 1ONM B 12 22 PDB 1ONM 1ONM 12 22 SEQRES 1 A 11 DG DC DT DT DC DA DG DT DC DG DT SEQRES 1 B 11 DA DC DG DA DC DG DG DA DA DG DC 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