Header list of 1s9o.pdb file
Complete list - 2 20 Bytes
HEADER DNA 05-FEB-04 1S9O
TITLE SOLUTION STRUCTURE OF THE NITROUS ACID INDUCED DNA INTERSTRAND CROSS-
TITLE 2 LINKED DODECAMER DUPLEX CGCTAC(G)TAGCG WITH THE CROSS-LINKED GUANINES
TITLE 3 DENOTED (G)
CAVEAT 1S9O RESIDUE DG B7 HAS EXTRA HYDROGEN ATOM H6
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*TP*AP*CP*GP*TP*AP*GP*CP*G)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICAL SYNTHESIS DESCRIBED IN HARWOOD ET AL. (1999)
SOURCE 4 J. AM. CHEM. SOC. 121, 5081-5082
KEYWDS DNA, NITROUS ACID, CROSS-LINK, EXTRAHELICAL CYTOSINES, MINOR GROOVE
EXPDTA SOLUTION NMR
NUMMDL 12
AUTHOR N.B.EDFELDT,E.A.HARWOOD,S.T.SIGURDSSON,P.B.HOPKINS,B.R.REID
REVDAT 4 02-MAR-22 1S9O 1 REMARK
REVDAT 3 26-MAY-10 1S9O 1 HET
REVDAT 2 24-FEB-09 1S9O 1 VERSN
REVDAT 1 01-NOV-05 1S9O 0
JRNL AUTH N.B.EDFELDT,E.A.HARWOOD,S.T.SIGURDSSON,P.B.HOPKINS,B.R.REID
JRNL TITL SOLUTION STRUCTURE OF A NITROUS ACID INDUCED DNA INTERSTRAND
JRNL TITL 2 CROSS-LINK.
JRNL REF NUCLEIC ACIDS RES. V. 32 2785 2004
JRNL REFN ISSN 0305-1048
JRNL PMID 15155847
JRNL DOI 10.1093/NAR/GKH606
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 1, DISCOVER 1
REMARK 3 AUTHORS : BRUKER (XWINNMR), BIOSYM (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 647 DISTANCE RESTRAINTS (514 ARE NOE-DERIVED, 42 FROM HYDROGEN
REMARK 3 BONDING, 81 REPULSIVE) AND 176 DIHEDRAL ANGLE RESTRAINTS (104
REMARK 3 BACKBONE, 72 CHIRAL).
REMARK 4
REMARK 4 1S9O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-04.
REMARK 100 THE DEPOSITION ID IS D_1000021541.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 200MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM DNA, 10MM PHOSPHATE PH 7.0,
REMARK 210 200MM NACL, 1MM EDTA; 1MM DNA,
REMARK 210 10MM PHOSPHATE PH 7.0, 200MM
REMARK 210 NACL, 1MM EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 1H-31P
REMARK 210 HETCOR
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : DMX; DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 1, DGII 1, DISCOVER 1,
REMARK 210 BIRDER 97
REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR
REMARK 210 DYNAMICS, MATRIX RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 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
REMARK 210 HOMONUCLEAR 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 400
REMARK 400 COMPOUND
REMARK 400 N2 ATOM OF G7 IS MISSING IN ALL MODELS DUE TO NITROUS ACID
REMARK 400 INDUCED DNA INTERSTRAND CROSS-LINKED DODECAMER DUPLEX
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-12
REMARK 470 RES CSSEQI ATOMS
REMARK 470 DG A 7 N2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 C2 DG A 7 N2 DG B 7 1.35
REMARK 500
REMARK 500 REMARK: NULL
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 DG B 7 C6 DG B 7 O6 0.127
REMARK 500 2 DG B 7 C6 DG B 7 O6 0.125
REMARK 500 3 DG B 7 C6 DG B 7 O6 0.127
REMARK 500 4 DG B 7 C6 DG B 7 O6 0.125
REMARK 500 5 DG B 7 C6 DG B 7 O6 0.126
REMARK 500 6 DG B 7 C6 DG B 7 O6 0.126
REMARK 500 7 DG A 7 C6 DG A 7 O6 0.126
REMARK 500 8 DG A 7 C6 DG A 7 O6 0.127
REMARK 500 9 DG A 7 C6 DG A 7 O6 0.127
REMARK 500 10 DG A 7 C6 DG A 7 O6 0.126
REMARK 500 11 DG A 7 C6 DG A 7 O6 0.126
REMARK 500 12 DG A 7 C6 DG A 7 O6 0.125
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 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 2 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.6 DEGREES
REMARK 500 2 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 3 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES
REMARK 500 3 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 4 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 4 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 4 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 4 DC B 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 186 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 DG A 2 0.06 SIDE CHAIN
REMARK 500 1 DC A 6 0.07 SIDE CHAIN
REMARK 500 1 DG A 12 0.07 SIDE CHAIN
REMARK 500 1 DG B 2 0.07 SIDE CHAIN
REMARK 500 1 DC B 6 0.07 SIDE CHAIN
REMARK 500 1 DG B 12 0.07 SIDE CHAIN
REMARK 500 2 DG A 2 0.06 SIDE CHAIN
REMARK 500 2 DC A 6 0.07 SIDE CHAIN
REMARK 500 2 DG A 12 0.07 SIDE CHAIN
REMARK 500 2 DG B 2 0.07 SIDE CHAIN
REMARK 500 2 DC B 6 0.07 SIDE CHAIN
REMARK 500 2 DG B 12 0.07 SIDE CHAIN
REMARK 500 3 DG A 2 0.06 SIDE CHAIN
REMARK 500 3 DC A 6 0.07 SIDE CHAIN
REMARK 500 3 DG A 12 0.07 SIDE CHAIN
REMARK 500 3 DG B 2 0.07 SIDE CHAIN
REMARK 500 3 DC B 6 0.07 SIDE CHAIN
REMARK 500 3 DG B 12 0.07 SIDE CHAIN
REMARK 500 4 DG A 2 0.07 SIDE CHAIN
REMARK 500 4 DC A 6 0.07 SIDE CHAIN
REMARK 500 4 DG A 12 0.08 SIDE CHAIN
REMARK 500 4 DG B 2 0.07 SIDE CHAIN
REMARK 500 4 DA B 9 0.05 SIDE CHAIN
REMARK 500 4 DG B 12 0.07 SIDE CHAIN
REMARK 500 5 DC A 6 0.07 SIDE CHAIN
REMARK 500 5 DG A 12 0.07 SIDE CHAIN
REMARK 500 5 DG B 2 0.07 SIDE CHAIN
REMARK 500 5 DC B 6 0.07 SIDE CHAIN
REMARK 500 5 DG B 12 0.07 SIDE CHAIN
REMARK 500 6 DG A 2 0.06 SIDE CHAIN
REMARK 500 6 DC A 6 0.07 SIDE CHAIN
REMARK 500 6 DG A 12 0.07 SIDE CHAIN
REMARK 500 6 DG B 2 0.06 SIDE CHAIN
REMARK 500 6 DC B 6 0.07 SIDE CHAIN
REMARK 500 6 DG B 12 0.07 SIDE CHAIN
REMARK 500 7 DG A 2 0.06 SIDE CHAIN
REMARK 500 7 DC A 6 0.07 SIDE CHAIN
REMARK 500 7 DG A 12 0.07 SIDE CHAIN
REMARK 500 7 DG B 2 0.06 SIDE CHAIN
REMARK 500 7 DC B 6 0.07 SIDE CHAIN
REMARK 500 7 DG B 12 0.07 SIDE CHAIN
REMARK 500 8 DG A 2 0.06 SIDE CHAIN
REMARK 500 8 DC A 6 0.07 SIDE CHAIN
REMARK 500 8 DG A 12 0.07 SIDE CHAIN
REMARK 500 8 DG B 2 0.06 SIDE CHAIN
REMARK 500 8 DC B 6 0.07 SIDE CHAIN
REMARK 500 8 DG B 12 0.07 SIDE CHAIN
REMARK 500 9 DG A 2 0.07 SIDE CHAIN
REMARK 500 9 DC A 6 0.07 SIDE CHAIN
REMARK 500 9 DG A 12 0.07 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 68 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1S9N RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE NITROUS ACID INDUCED DNA INTERSTRAND
REMARK 900 CROSS-LINKED DODECAMER DUPLEX GCATCC(G)GATGC WITH THE CROSS-LINKED
REMARK 900 GUANINES DENOTED (G)
DBREF 1S9O A 1 12 PDB 1S9O 1S9O 1 12
DBREF 1S9O B 1 12 PDB 1S9O 1S9O 1 12
SEQRES 1 A 12 DC DG DC DT DA DC DG DT DA DG DC DG
SEQRES 1 B 12 DC DG DC DT DA DC DG DT DA DG DC DG
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