HEADER DNA 26-SEP-01 1K29 TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING M1G OPPOSITE A 2 BASE TITLE 2 PAIR DELETION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*TP*CP*GP*CP*(M1G)P*CP*GP*GP*CP*AP*TP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*AP*TP*GP*CP*CP*GP*CP*GP*AP*T)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THE SALMONELLA SOURCE 4 TYPHIMURIUM HIS3052 GENE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THE SALMONELLA SOURCE 8 TYPHIMURIUM HIS3052 GENE KEYWDS TWO BASE DELETION, DNA ADDUCT, MALONDIALDEHYDE, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR N.C.SCHNETZ-BOUTAUD,S.SALEH,L.J.MARNETT,M.P.STONE REVDAT 5 22-MAY-24 1K29 1 REMARK REVDAT 4 23-FEB-22 1K29 1 REMARK LINK REVDAT 3 24-FEB-09 1K29 1 VERSN REVDAT 2 01-APR-03 1K29 1 JRNL REVDAT 1 16-JAN-02 1K29 0 JRNL AUTH N.C.SCHNETZ-BOUTAUD,S.SALEH,L.J.MARNETT,M.P.STONE JRNL TITL THE EXOCYCLIC 1,N2-DEOXYGUANOSINE PYRIMIDOPURINONE M1G IS A JRNL TITL 2 CHEMICALLY STABLE DNA ADDUCT WHEN PLACED OPPOSITE A TWO-BASE JRNL TITL 3 DELETION IN THE (CPG)3 FRAMESHIFT HOTSPOT OF THE SALMONELLA JRNL TITL 4 TYPHIMURIUM HISD3052 GENE. JRNL REF BIOCHEMISTRY V. 40 15638 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11747439 JRNL DOI 10.1021/BI011242U REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.85 REMARK 3 AUTHORS : BRUKER INSTRUMENT (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014469. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 303; 278 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 0.1M NACL; 0.1M NACL; 0.1M NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DNA, 10MM PHOSPHATE BUFFER, REMARK 210 0.1M NACL, 50 UM EDTA , PH 7; REMARK 210 2MM DNA, 10MM PHOSPHATE BUFFER, REMARK 210 0.1M NACL, 50 UM EDTA , PH 7 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; E-COSY; P-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, MARDIGRAS 3.0, X REMARK 210 -PLOR 3.85 REMARK 210 METHOD USED : MATRIX RELAXATION, SIMULATED REMARK 210 ANNEALING, DISTANCE RESTRAINTS, REMARK 210 DIHEDRAL ANGLE RESTRAINTS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED STRUCTURE IS AN REMARK 210 AVERAGE OF 10 DIFFERENT REMARK 210 STRUCTURES THAT WERE BACK REMARK 210 CALCULATED AND THE DATA AGREED REMARK 210 WITH EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND REMARK 210 HETERO- NUCLEAR 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 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 3 C4 DC A 3 C5 -0.055 REMARK 500 DC A 5 C4 DC A 5 C5 -0.059 REMARK 500 DC A 7 C4 DC A 7 C5 -0.057 REMARK 500 DC A 10 C4 DC A 10 C5 -0.056 REMARK 500 DC B 14 C4 DC B 14 C5 -0.054 REMARK 500 DC B 18 C4 DC B 18 C5 -0.054 REMARK 500 DC B 19 C4 DC B 19 C5 -0.054 REMARK 500 DC B 21 C4 DC B 21 C5 -0.055 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT A 2 C4 - C5 - C6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 11 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT A 12 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 12 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 13 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 16 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 17 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 20 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA B 23 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 23 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 24 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 24 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 24 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1K29 A 1 13 PDB 1K29 1K29 1 13 DBREF 1K29 B 14 24 PDB 1K29 1K29 14 24 SEQRES 1 A 13 DA DT DC DG DC M1G DC DG DG DC DA DT DG SEQRES 1 B 11 DC DA DT DG DC DC DG DC DG DA DT MODRES 1K29 M1G A 6 DG HET M1G A 6 36 HETNAM M1G 3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE- HETNAM 2 M1G 10-ONE-5'-MONOPHOSPHATE FORMUL 1 M1G C13 H14 N5 O7 P LINK O3' DC A 5 P M1G A 6 1555 1555 1.61 LINK O3' M1G 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