Header list of 1jrv.pdb file
Complete list - b 23 2 Bytes
HEADER DNA 15-AUG-01 1JRV
TITLE SOLUTION STRUCTURE OF DAATAA DNA BULGE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*AP*AP*GP*CP*TP*AP*CP*G)-
COMPND 3 3';
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3';
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DNA BULGE, FIVE-NUCLEOTIDE BULGE LOOP, DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN,S.DIEKMANN,
AUTHOR 2 H.FRITZSCHE
REVDAT 3 23-FEB-22 1JRV 1 REMARK
REVDAT 2 24-FEB-09 1JRV 1 VERSN
REVDAT 1 19-JUN-02 1JRV 0
JRNL AUTH F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN,S.DIEKMANN,
JRNL AUTH 2 H.FRITZSCHE
JRNL TITL SOLUTION STRUCTURE OF DAATAA AND DAAUAA DNA BULGES.
JRNL REF NUCLEIC ACIDS RES. V. 30 2669 2002
JRNL REFN ISSN 0305-1048
JRNL PMID 12060684
JRNL DOI 10.1093/NAR/GKF375
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 3, AMBER 5.0
REMARK 3 AUTHORS : DELAGLIO, F. ET AL. (NMRPIPE), WEINER, S.J.,
REMARK 3 KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A. (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 906 RESTRAINTS, 645 ARE NOE-
REMARK 3 DERIVED
REMARK 3 DISTANCE CONSTRAINTS, 235 DIHEDRAL ANGLE RESTRAINTS, 26 DISTANCE
REMARK 3 RESTRAINTS
REMARK 3 FROM HYDROGEN BONDS.
REMARK 4
REMARK 4 1JRV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-01.
REMARK 100 THE DEPOSITION ID IS D_1000014116.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300; 278
REMARK 210 PH : 7; 7
REMARK 210 IONIC STRENGTH : 100MM NA+; 100MM NA+
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.6MM IN DUPLEX; 10MM PHOSPHATE
REMARK 210 BUFFER; 100MM NACL; 0.05MM EDTA;
REMARK 210 100% D2O; 1.6MM IN DUPLEX; 10MM
REMARK 210 PHOSPHATE BUFFER; 100MM NACL;
REMARK 210 0.05MM EDTA; 90% H2O, 10% D2O;
REMARK 210 1.6MM IN DUPLEX; 100MM NACL;
REMARK 210 0.05MM EDTA; 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_NOESY; E-COSY; 31P
REMARK 210 -1H_CORRELATED
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS 3.2, DYANA 1.5, CURVES
REMARK 210 4.0, AMBER 5.0
REMARK 210 METHOD USED : MATRIX RELAXATION (MARDIGRAS);
REMARK 210 TORSION ANGLE DYNAMICS (DYANA);
REMARK 210 ENERGY MINIMIZATION (AMBER)
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 400
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
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 AND HETERONUCLEAR 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 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DC A 13 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DT B 27 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DC B 29 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES
REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DT A 9 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES
REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 2 DC A 13 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DA B 26 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DT B 27 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 2 DC B 29 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.8 DEGREES
REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 3 DA A 10 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES
REMARK 500 3 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 3 DC A 13 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 DA A 15 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES
REMARK 500 3 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 3 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 3 DA B 26 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 3 DC B 29 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 4 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES
REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 4 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES
REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 218 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 DA A 3 0.12 SIDE CHAIN
REMARK 500 1 DT A 4 0.09 SIDE CHAIN
REMARK 500 1 DC A 13 0.08 SIDE CHAIN
REMARK 500 1 DG B 19 0.07 SIDE CHAIN
REMARK 500 1 DA B 26 0.05 SIDE CHAIN
REMARK 500 1 DT B 27 0.07 SIDE CHAIN
REMARK 500 2 DC A 5 0.06 SIDE CHAIN
REMARK 500 2 DG B 19 0.09 SIDE CHAIN
REMARK 500 2 DT B 27 0.08 SIDE CHAIN
REMARK 500 3 DT A 9 0.06 SIDE CHAIN
REMARK 500 3 DG B 19 0.09 SIDE CHAIN
REMARK 500 3 DG B 25 0.08 SIDE CHAIN
REMARK 500 3 DT B 27 0.07 SIDE CHAIN
REMARK 500 4 DC B 18 0.07 SIDE CHAIN
REMARK 500 4 DG B 19 0.09 SIDE CHAIN
REMARK 500 4 DT B 27 0.08 SIDE CHAIN
REMARK 500 5 DG A 17 0.05 SIDE CHAIN
REMARK 500 5 DG B 19 0.09 SIDE CHAIN
REMARK 500 5 DT B 27 0.08 SIDE CHAIN
REMARK 500 6 DC A 5 0.06 SIDE CHAIN
REMARK 500 6 DG B 19 0.10 SIDE CHAIN
REMARK 500 6 DT B 27 0.07 SIDE CHAIN
REMARK 500 7 DC A 5 0.07 SIDE CHAIN
REMARK 500 7 DG B 19 0.08 SIDE CHAIN
REMARK 500 7 DT B 27 0.06 SIDE CHAIN
REMARK 500 8 DC A 5 0.06 SIDE CHAIN
REMARK 500 8 DC B 18 0.07 SIDE CHAIN
REMARK 500 8 DG B 19 0.07 SIDE CHAIN
REMARK 500 8 DT B 27 0.07 SIDE CHAIN
REMARK 500 9 DG A 17 0.05 SIDE CHAIN
REMARK 500 9 DG B 19 0.09 SIDE CHAIN
REMARK 500 9 DG B 25 0.07 SIDE CHAIN
REMARK 500 9 DT B 27 0.07 SIDE CHAIN
REMARK 500 10 DT A 4 0.08 SIDE CHAIN
REMARK 500 10 DC A 5 0.06 SIDE CHAIN
REMARK 500 10 DG B 19 0.09 SIDE CHAIN
REMARK 500 10 DG B 25 0.06 SIDE CHAIN
REMARK 500 10 DT B 27 0.07 SIDE CHAIN
REMARK 500 11 DA A 3 0.05 SIDE CHAIN
REMARK 500 11 DT A 4 0.07 SIDE CHAIN
REMARK 500 11 DC A 13 0.07 SIDE CHAIN
REMARK 500 11 DG B 19 0.09 SIDE CHAIN
REMARK 500 11 DC B 24 0.07 SIDE CHAIN
REMARK 500 11 DG B 25 0.08 SIDE CHAIN
REMARK 500 11 DT B 27 0.08 SIDE CHAIN
REMARK 500 12 DG A 17 0.07 SIDE CHAIN
REMARK 500 12 DG B 19 0.10 SIDE CHAIN
REMARK 500 12 DT B 27 0.07 SIDE CHAIN
REMARK 500 13 DC A 5 0.06 SIDE CHAIN
REMARK 500 13 DG B 19 0.10 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 58 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1QSK RELATED DB: PDB
REMARK 900 1QSK CONTAINS A SIMILAR PENTANUCLEOTIDE DNA BULGE WITH AAAAA IN THE
REMARK 900 BULGE LOOP.
REMARK 900 RELATED ID: 1JRW RELATED DB: PDB
REMARK 900 1JRW IS THE SOLUTION STRUCTURE OF DAATAA DNA BULGE (MINIMIZED
REMARK 900 AVERAGE STRUCTURE)
REMARK 900 RELATED ID: 1JS5 RELATED DB: PDB
REMARK 900 1JS5 IS THE SOLUTION STRUCTURE OF DAAUAA DNA BULGE (MINIMIZED
REMARK 900 AVERAGE STRUCTURE)
REMARK 900 RELATED ID: 1JS7 RELATED DB: PDB
REMARK 900 1JS7 IS THE SOLUTION STRUCTURE OF DAAUAA DNA BULGE (ENSEMBLE)
DBREF 1JRV A 1 17 PDB 1JRV 1JRV 1 17
DBREF 1JRV B 18 29 PDB 1JRV 1JRV 18 29
SEQRES 1 A 17 DG DC DA DT DC DG DA DA DT DA DA DG DC
SEQRES 2 A 17 DT DA DC DG
SEQRES 1 B 12 DC DG DT DA DG DC DC DG DA DT DG DC
CRYST1 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 - b 23 2 Bytes