Header list of 1pib.pdb file
Complete list - 23 20 Bytes
HEADER DNA 30-MAY-03 1PIB
TITLE SOLUTION STRUCTURE OF DNA CONTAINING CPD OPPOSITED BY GA
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*AP*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 CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER, CPD CONTAINING DNA, HELICAL
KEYWDS 2 DISTORTION, THYMINEDIMER, DNA
EXPDTA SOLUTION NMR
NUMMDL 16
AUTHOR J.H.LEE,C.J.PARK,J.S.SHIN,B.S.CHOI
REVDAT 3 23-FEB-22 1PIB 1 REMARK LINK
REVDAT 2 24-FEB-09 1PIB 1 VERSN
REVDAT 1 18-MAY-04 1PIB 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, X-PLOR 3.1
REMARK 3 AUTHORS : FRANK DELAGLIO (NMRPIPE), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1PIB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUN-03.
REMARK 100 THE DEPOSITION ID IS D_1000019339.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 277; 300; 290
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 DNA, 20MM PHOSPHATE BUFFER;
REMARK 210 1MM DNA, 20MM PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR 3.1, SPARKY 3.106
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY
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 A 4 N9 DA A 4 C4 0.045
REMARK 500 1 DT A 5 N1 DT A 5 C2 0.069
REMARK 500 1 DT A 5 C2 DT A 5 N3 0.050
REMARK 500 1 DT A 5 C4 DT A 5 C5 0.085
REMARK 500 1 DT A 5 C5 DT A 5 C6 0.255
REMARK 500 1 DT A 6 N1 DT A 6 C2 0.058
REMARK 500 1 DT A 6 C4 DT A 6 C5 0.072
REMARK 500 1 DT A 6 C5 DT A 6 C6 0.237
REMARK 500 1 DT A 6 C6 DT A 6 N1 0.061
REMARK 500 2 DA A 4 N9 DA A 4 C4 0.044
REMARK 500 2 DT A 5 N1 DT A 5 C2 0.069
REMARK 500 2 DT A 5 C4 DT A 5 C5 0.081
REMARK 500 2 DT A 5 C5 DT A 5 C6 0.256
REMARK 500 2 DT A 6 N1 DT A 6 C2 0.060
REMARK 500 2 DT A 6 C4 DT A 6 C5 0.069
REMARK 500 2 DT A 6 C5 DT A 6 C6 0.245
REMARK 500 2 DT A 6 C6 DT A 6 N1 0.065
REMARK 500 2 DT B 17 N1 DT B 17 C2 0.049
REMARK 500 3 DA A 4 N9 DA A 4 C4 0.045
REMARK 500 3 DT A 5 N1 DT A 5 C2 0.075
REMARK 500 3 DT A 5 C2 DT A 5 N3 0.056
REMARK 500 3 DT A 5 C4 DT A 5 C5 0.080
REMARK 500 3 DT A 5 C5 DT A 5 C6 0.258
REMARK 500 3 DT A 5 C5 DT A 5 C7 0.037
REMARK 500 3 DT A 6 N1 DT A 6 C2 0.058
REMARK 500 3 DT A 6 C4 DT A 6 C5 0.070
REMARK 500 3 DT A 6 C5 DT A 6 C6 0.239
REMARK 500 3 DT A 6 C6 DT A 6 N1 0.063
REMARK 500 3 DT B 17 N1 DT B 17 C2 0.052
REMARK 500 4 DA A 4 N9 DA A 4 C4 0.041
REMARK 500 4 DT A 5 N1 DT A 5 C2 0.068
REMARK 500 4 DT A 5 C2 DT A 5 N3 0.050
REMARK 500 4 DT A 5 C4 DT A 5 C5 0.086
REMARK 500 4 DT A 5 C5 DT A 5 C6 0.257
REMARK 500 4 DT A 6 N1 DT A 6 C2 0.059
REMARK 500 4 DT A 6 C4 DT A 6 C5 0.072
REMARK 500 4 DT A 6 C5 DT A 6 C6 0.237
REMARK 500 4 DT A 6 C6 DT A 6 N1 0.060
REMARK 500 5 DA A 4 N9 DA A 4 C4 0.039
REMARK 500 5 DT A 5 N1 DT A 5 C2 0.069
REMARK 500 5 DT A 5 C2 DT A 5 N3 0.053
REMARK 500 5 DT A 5 C4 DT A 5 C5 0.082
REMARK 500 5 DT A 5 C5 DT A 5 C6 0.255
REMARK 500 5 DT A 6 N1 DT A 6 C2 0.061
REMARK 500 5 DT A 6 C4 DT A 6 C5 0.068
REMARK 500 5 DT A 6 C5 DT A 6 C6 0.237
REMARK 500 5 DT A 6 C6 DT A 6 N1 0.063
REMARK 500 6 DA A 4 N9 DA A 4 C4 0.043
REMARK 500 6 DT A 5 N1 DT A 5 C2 0.071
REMARK 500 6 DT A 5 C2 DT A 5 N3 0.055
REMARK 500
REMARK 500 THIS ENTRY HAS 149 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 DG A 2 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 14.2 DEGREES
REMARK 500 1 DC A 3 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES
REMARK 500 1 DA A 4 C3' - O3' - P ANGL. DEV. = 13.5 DEGREES
REMARK 500 1 DT A 5 C4 - C5 - C6 ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = -9.0 DEGREES
REMARK 500 1 DT A 5 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES
REMARK 500 1 DT A 6 C5 - C6 - N1 ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -16.3 DEGREES
REMARK 500 1 DT A 6 C3' - O3' - P ANGL. DEV. = 14.6 DEGREES
REMARK 500 1 DC A 8 C3' - O3' - P ANGL. DEV. = 14.9 DEGREES
REMARK 500 1 DG A 9 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DG A 9 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES
REMARK 500 1 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 DC B 12 P - O5' - C5' ANGL. DEV. = 9.8 DEGREES
REMARK 500 1 DC B 12 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES
REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES
REMARK 500 1 DT B 14 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES
REMARK 500 1 DG B 15 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 DG B 15 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES
REMARK 500 1 DA B 16 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES
REMARK 500 1 DT B 17 C3' - O3' - P ANGL. DEV. = 13.2 DEGREES
REMARK 500 1 DG B 18 P - O5' - C5' ANGL. DEV. = 10.5 DEGREES
REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DG B 18 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES
REMARK 500 1 DC B 19 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES
REMARK 500 1 DG B 20 N3 - C2 - N2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES
REMARK 500 2 DC A 3 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES
REMARK 500 2 DC A 3 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES
REMARK 500 2 DA A 4 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES
REMARK 500 2 DT A 5 C4 - C5 - C6 ANGL. DEV. = -6.5 DEGREES
REMARK 500 2 DT A 5 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DT A 5 C4 - C5 - C7 ANGL. DEV. = -9.8 DEGREES
REMARK 500 2 DT A 5 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES
REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES
REMARK 500 2 DT A 6 C5 - C6 - N1 ANGL. DEV. = -7.7 DEGREES
REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -14.9 DEGREES
REMARK 500 2 DT A 6 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES
REMARK 500 2 DA A 7 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 2 DC A 8 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES
REMARK 500 2 DG A 9 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DG A 9 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES
REMARK 500 2 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES
REMARK 500 2 DC B 12 P - O5' - C5' ANGL. DEV. = 9.6 DEGREES
REMARK 500 2 DC B 12 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES
REMARK 500 2 DG B 13 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES
REMARK 500 2 DT B 14 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 479 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 0.33 SIDE CHAIN
REMARK 500 2 DT A 5 0.09 SIDE CHAIN
REMARK 500 2 DT A 6 0.29 SIDE CHAIN
REMARK 500 3 DT A 5 0.08 SIDE CHAIN
REMARK 500 3 DT A 6 0.33 SIDE CHAIN
REMARK 500 4 DT A 5 0.09 SIDE CHAIN
REMARK 500 4 DT A 6 0.34 SIDE CHAIN
REMARK 500 5 DT A 5 0.09 SIDE CHAIN
REMARK 500 5 DT A 6 0.33 SIDE CHAIN
REMARK 500 6 DT A 5 0.09 SIDE CHAIN
REMARK 500 6 DT A 6 0.33 SIDE CHAIN
REMARK 500 7 DT A 5 0.08 SIDE CHAIN
REMARK 500 7 DT A 6 0.28 SIDE CHAIN
REMARK 500 8 DT A 5 0.09 SIDE CHAIN
REMARK 500 8 DT A 6 0.34 SIDE CHAIN
REMARK 500 9 DT A 5 0.09 SIDE CHAIN
REMARK 500 9 DT A 6 0.32 SIDE CHAIN
REMARK 500 10 DT A 5 0.08 SIDE CHAIN
REMARK 500 10 DT A 6 0.31 SIDE CHAIN
REMARK 500 11 DT A 5 0.09 SIDE CHAIN
REMARK 500 11 DT A 6 0.32 SIDE CHAIN
REMARK 500 12 DT A 5 0.08 SIDE CHAIN
REMARK 500 12 DT A 6 0.31 SIDE CHAIN
REMARK 500 13 DT A 5 0.09 SIDE CHAIN
REMARK 500 13 DT A 6 0.33 SIDE CHAIN
REMARK 500 14 DT A 5 0.09 SIDE CHAIN
REMARK 500 14 DT A 6 0.29 SIDE CHAIN
REMARK 500 15 DT A 5 0.09 SIDE CHAIN
REMARK 500 15 DT A 6 0.27 SIDE CHAIN
REMARK 500 16 DT A 5 0.08 SIDE CHAIN
REMARK 500 16 DT A 6 0.29 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1SNH RELATED DB: PDB
REMARK 900 REFERRED TO AS THE CPD/GG DUPLEX
DBREF 1PIB A 1 10 PDB 1PIB 1PIB 1 10
DBREF 1PIB B 11 20 PDB 1PIB 1PIB 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 DA DT DG DC DG
LINK C5 DT A 5 C5 DT A 6 1555 1555 1.65
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 - 23 20 Bytes