Header list of 1k29.pdb file
Complete list - 23 202 Bytes
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 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
Complete list - 23 202 Bytes