Header list of 1dk9.pdb file
Complete list - 16 202 Bytes
HEADER DNA 06-DEC-99 1DK9
TITLE SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(CP*AP*TP*GP*AP*GP*TP*AP*CP*)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(GP*TP*AP*CP*TP*CP*AP*TP*GP*)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED
KEYWDS DNA, DUPLEX
EXPDTA SOLUTION NMR
AUTHOR D.A.KLEWER,A.HOSKINS,V.J.DAVISSON,D.E.BERGSTROM,A.C.LIWANG
REVDAT 5 16-FEB-22 1DK9 1 REMARK
REVDAT 4 24-FEB-09 1DK9 1 VERSN
REVDAT 3 01-APR-03 1DK9 1 JRNL
REVDAT 2 03-NOV-00 1DK9 1 JRNL REMARK
REVDAT 1 16-DEC-99 1DK9 0
JRNL AUTH D.A.KLEWER,A.HOSKINS,P.ZHANG,V.J.DAVISSON,D.E.BERGSTROM,
JRNL AUTH 2 A.C.LIWANG
JRNL TITL NMR STRUCTURE OF A DNA DUPLEX CONTAINING NUCLEOSIDE ANALOG
JRNL TITL 2 1-(2'-DEOXY-BETA-D-RIBOFURANOSYL)-3-NITROPYRROLE AND THE
JRNL TITL 3 STRUCTURE OF THE UNMODIFIED CONTROL.
JRNL REF NUCLEIC ACIDS RES. V. 28 4514 2000
JRNL REFN ISSN 0305-1048
JRNL PMID 11071940
JRNL DOI 10.1093/NAR/28.22.4514
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR V3.840
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-99.
REMARK 100 THE DEPOSITION ID IS D_1000010154.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278
REMARK 210 PH : 7
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 4.5MM DUPLEX, 100MM NACL, 10MM
REMARK 210 NAOP, 1MM EDTA
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 : CORMA 5.2, MARDIGRAS 5.2,
REMARK 210 NMRPIPE 7.1, VNMR 6.1B, PIPP
REMARK 210 4.2.7
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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: 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 H21 DG A 6 O2 DC B 13 1.40
REMARK 500 H21 DG A 4 O2 DC B 15 1.47
REMARK 500 O2 DC A 1 H21 DG B 18 1.48
REMARK 500 O2 DC A 9 H21 DG B 10 1.50
REMARK 500 O6 DG A 4 H41 DC B 15 1.50
REMARK 500 H41 DC A 9 O6 DG B 10 1.54
REMARK 500 H1 DG A 6 N3 DC B 13 1.54
REMARK 500 H1 DG A 4 N3 DC B 15 1.55
REMARK 500 N1 DA A 8 H3 DT B 11 1.56
REMARK 500 N1 DA A 5 H3 DT B 14 1.56
REMARK 500 N1 DA A 2 H3 DT B 17 1.58
REMARK 500 O6 DG A 6 H41 DC B 13 1.58
REMARK 500 N3 DC A 1 H1 DG B 18 1.58
REMARK 500 O4 DT A 7 H61 DA B 12 1.59
REMARK 500 H3 DT A 7 N1 DA B 12 1.59
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 DT A 7 C5 DT A 7 C7 0.046
REMARK 500 DT B 17 C5 DT B 17 C7 0.038
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 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DC A 9 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES
REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES
REMARK 500 DA B 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DA B 16 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DG B 18 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES
REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DK6 RELATED DB: PDB
REMARK 900 RESIDUE 14 IS REPLACED BY 3-NITROPYRROLE
DBREF 1DK9 A 1 9 PDB 1DK9 1DK9 1 9
DBREF 1DK9 B 10 18 PDB 1DK9 1DK9 10 18
SEQRES 1 A 9 DC DA DT DG DA DG DT DA DC
SEQRES 1 B 9 DG DT DA DC DT DC DA DT 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
Complete list - 16 202 Bytes