10 20 30 40 50 60 70 80 1K29 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 26-SEP-01 1K29
TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING M1G OPPOSITE TITLE 2 A 2 BASE 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)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*AP*TP*GP*CP*CP*GP*CP*GP*AP*T)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THE SOURCE 4 SALMONELLA TYPHIMURIUM HIS3052 GENE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THE SOURCE 8 SALMONELLA TYPHIMURIUM HIS3052 GENE
KEYWDS TWO BASE DELETION, DNA ADDUCT, MALONDIALDEHYDE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR N.C.SCHNETZ-BOUTAUD,S.SALEH,L.J.MARNETT,M.P.STONE
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 JRNL TITL 2 M1G IS A CHEMICALLY STABLE DNA ADDUCT WHEN PLACED JRNL TITL 3 OPPOSITE A TWO-BASE DELETION IN THE (CPG)3 JRNL TITL 4 FRAMESHIFT HOTSPOT OF THE SALMONELLA TYPHIMURIUM JRNL TITL 5 HISD3052 GENE. JRNL REF BIOCHEMISTRY V. 40 15638 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11747439 JRNL DOI 10.1021/BI011242U
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.85 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1K29 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-01. REMARK 100 THE RCSB ID CODE IS RCSB014469.
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 REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DNA, 10MM PHOSPHATE REMARK 210 BUFFER, 0.1M NACL, 50 UM EDTA REMARK 210 , PH 7; 2MM DNA, 10MM REMARK 210 PHOSPHATE BUFFER, 0.1M NACL, REMARK 210 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 : XWINNMR 2.6, FELIX 2000, REMARK 210 MARDIGRAS 3.0, X-PLOR 3.85 REMARK 210 METHOD USED : MATRIX RELAXATION, REMARK 210 SIMULATED ANNEALING, DISTANCE REMARK 210 RESTRAINTS, DIHEDRAL ANGLE REMARK 210 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 REMARK 210 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- REMARK 210 AND 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 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. = 4.4 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. = 2.4 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.6 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