Header list of 1snh.pdb file
Complete list - 2 20 Bytes
HEADER DNA 11-MAR-04 1SNH TITLE SOLUTION STRUCTURE OF THE DNA DECAMER DUPLEX CONTAINING DOUBLE TG TITLE 2 MISMATCHES OF CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*AP*TP*TP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*GP*TP*GP*GP*TP*GP*CP*G)-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 DNA, G-T MISMATCH, CPD, MAJOR GROOVE WIDENING EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR J.H.LEE,C.J.PARK,J.S.SHIN,T.IKEGAMI,H.AKUTSU,B.S.CHOI REVDAT 3 02-MAR-22 1SNH 1 REMARK LINK REVDAT 2 24-FEB-09 1SNH 1 VERSN REVDAT 1 18-MAY-04 1SNH 0 JRNL AUTH J.H.LEE,C.J.PARK,J.S.SHIN,T.IKEGAMI,H.AKUTSU,B.S.CHOI JRNL TITL NMR STRUCTURE OF THE DNA DECAMER DUPLEX CONTAINING DOUBLE JRNL TITL 2 T*G MISMATCHES OF CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER: JRNL TITL 3 IMPLICATIONS FOR DNA DAMAGE RECOGNITION BY THE XPC-HHR23B JRNL TITL 4 COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 32 2474 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15121904 JRNL DOI 10.1093/NAR/GKH568 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.1, XPLOR-NIH 2.9.4A REMARK 3 AUTHORS : F. DELAGLIO, S. GRZESIEK, G. W. VUISTER, G. ZHU, REMARK 3 J. PFEIFER AND A. BAX (NMRPIPE), G. MARIUS CLORE , REMARK 3 JOHN KUSZEWSKI, CHARLES D. SCHWIETERS, AND NICO REMARK 3 TJANDRA (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A 500 NOE REMARK 3 -DERIVED DISTANCE CONSTRAINTS, 112 DIHEDRAL ANGLE RESTRAINTS, 13 REMARK 3 RESIDUAL DIPOLAR COUPLING RESTRAINTS REMARK 4 REMARK 4 1SNH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021852. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 274; 290; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL; 100MM NACL; 100MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM CPD/GG DUPLEX, NONLABELED, REMARK 210 20MM PHOSPHATE BUFFER, 100MM REMARK 210 NACL, 90% H2O, 10% D20; 1MM CPD/ REMARK 210 GG DUPLEX, NONLABELED, 20MM REMARK 210 PHOSPHATE BUFFER, 100MM NACL, REMARK 210 100% D2O; 1MM CPD/GG DUPLEX, REMARK 210 NONLABELED, 20MM PHOSPHATE REMARK 210 BUFFER, 100MM NACL, 100% D2O, REMARK 210 15MG/ML PF1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 NATURAL ABUNDANCE 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 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 DT A 5 N1 DT A 5 C2 0.081 REMARK 500 1 DT A 5 C4 DT A 5 C5 0.080 REMARK 500 1 DT A 5 C5 DT A 5 C6 0.239 REMARK 500 1 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 1 DT A 6 N1 DT A 6 C2 0.053 REMARK 500 1 DT A 6 C4 DT A 6 C5 0.069 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.260 REMARK 500 1 DT A 6 C6 DT A 6 N1 0.066 REMARK 500 1 DT A 6 C5 DT A 6 C7 0.041 REMARK 500 1 DT B 17 N1 DT B 17 C2 0.049 REMARK 500 2 DT A 5 N1 DT A 5 C2 0.075 REMARK 500 2 DT A 5 C4 DT A 5 C5 0.081 REMARK 500 2 DT A 5 C5 DT A 5 C6 0.237 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.038 REMARK 500 2 DT A 6 N1 DT A 6 C2 0.055 REMARK 500 2 DT A 6 C4 DT A 6 C5 0.072 REMARK 500 2 DT A 6 C5 DT A 6 C6 0.259 REMARK 500 2 DT A 6 C6 DT A 6 N1 0.059 REMARK 500 2 DT B 17 N1 DT B 17 C2 0.052 REMARK 500 3 DT A 5 N1 DT A 5 C2 0.069 REMARK 500 3 DT A 5 C4 DT A 5 C5 0.081 REMARK 500 3 DT A 5 C5 DT A 5 C6 0.239 REMARK 500 3 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 3 DT A 6 N1 DT A 6 C2 0.053 REMARK 500 3 DT A 6 C4 DT A 6 C5 0.077 REMARK 500 3 DT A 6 C5 DT A 6 C6 0.255 REMARK 500 3 DT A 6 C6 DT A 6 N1 0.052 REMARK 500 3 DT B 17 N1 DT B 17 C2 0.049 REMARK 500 4 DT A 5 N1 DT A 5 C2 0.074 REMARK 500 4 DT A 5 C4 DT A 5 C5 0.081 REMARK 500 4 DT A 5 C5 DT A 5 C6 0.239 REMARK 500 4 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 4 DT A 6 N1 DT A 6 C2 0.057 REMARK 500 4 DT A 6 C4 DT A 6 C5 0.072 REMARK 500 4 DT A 6 C5 DT A 6 C6 0.259 REMARK 500 4 DT A 6 C6 DT A 6 N1 0.060 REMARK 500 4 DT B 17 N1 DT B 17 C2 0.051 REMARK 500 5 DT A 5 N1 DT A 5 C2 0.074 REMARK 500 5 DT A 5 C4 DT A 5 C5 0.079 REMARK 500 5 DT A 5 C5 DT A 5 C6 0.242 REMARK 500 5 DT A 5 C5 DT A 5 C7 0.036 REMARK 500 5 DT A 6 N1 DT A 6 C2 0.058 REMARK 500 5 DT A 6 C4 DT A 6 C5 0.070 REMARK 500 5 DT A 6 C5 DT A 6 C6 0.259 REMARK 500 5 DT A 6 C6 DT A 6 N1 0.060 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.038 REMARK 500 6 DT A 5 N1 DT A 5 C2 0.074 REMARK 500 6 DT A 5 C4 DT A 5 C5 0.080 REMARK 500 6 DT A 5 C5 DT A 5 C6 0.239 REMARK 500 6 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 REMARK 500 THIS ENTRY HAS 103 BOND DEVIATIONS. 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 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT A 5 C5 - C6 - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 5 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 5 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DT A 5 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DT A 6 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 6 C5 - C6 - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -13.3 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 15 N3 - C2 - N2 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG B 16 N3 - C2 - N2 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG B 20 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DT A 5 C4 - C5 - C6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DT A 5 C5 - C6 - N1 ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DT A 5 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 5 C4 - C5 - C7 ANGL. DEV. = -7.8 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -7.9 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DT A 6 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 6 C5 - C6 - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -14.1 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 11 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG B 15 N3 - C2 - N2 ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DG B 16 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DG B 16 N3 - C2 - N2 ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG B 18 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DC B 19 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG B 20 N3 - C2 - N2 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 262 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 DT A 5 0.09 SIDE CHAIN REMARK 500 1 DT A 6 0.24 SIDE CHAIN REMARK 500 2 DT A 5 0.10 SIDE CHAIN REMARK 500 2 DT A 6 0.28 SIDE CHAIN REMARK 500 3 DT A 5 0.11 SIDE CHAIN REMARK 500 3 DT A 6 0.31 SIDE CHAIN REMARK 500 4 DT A 5 0.10 SIDE CHAIN REMARK 500 4 DT A 6 0.28 SIDE CHAIN REMARK 500 5 DT A 5 0.11 SIDE CHAIN REMARK 500 5 DT A 6 0.22 SIDE CHAIN REMARK 500 6 DT A 5 0.10 SIDE CHAIN REMARK 500 6 DT A 6 0.28 SIDE CHAIN REMARK 500 7 DT A 5 0.09 SIDE CHAIN REMARK 500 7 DT A 6 0.27 SIDE CHAIN REMARK 500 8 DT A 5 0.10 SIDE CHAIN REMARK 500 8 DT A 6 0.29 SIDE CHAIN REMARK 500 9 DT A 5 0.10 SIDE CHAIN REMARK 500 9 DT A 6 0.29 SIDE CHAIN REMARK 500 10 DT A 5 0.11 SIDE CHAIN REMARK 500 10 DT A 6 0.25 SIDE CHAIN REMARK 500 11 DT A 5 0.12 SIDE CHAIN REMARK 500 11 DT A 6 0.26 SIDE CHAIN REMARK 500 12 DT A 5 0.11 SIDE CHAIN REMARK 500 12 DT A 6 0.28 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PIB RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE DNA DECAMER DUPLEX CONTAINING SINGLE TG REMARK 900 MISMATCHES OF CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER DBREF 1SNH A 1 10 PDB 1SNH 1SNH 1 10 DBREF 1SNH B 11 20 PDB 1SNH 1SNH 11 20 SEQRES 1 A 10 DC DG DC DA DT DT DA DC DG DC SEQRES 1 B 10 DG DC DG DT DG DG DT DG DC DG LINK C5 DT A 5 C5 DT A 6 1555 1555 1.66 LINK C6 DT A 5 C6 DT A 6 1555 1555 1.64 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
Complete list - 2 20 Bytes