Header list of 1drn.pdb file
Complete list - 16 202 Bytes
HEADER DNA-RNA HYBRID 15-NOV-95 1DRN
TITLE NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID
TITLE 2 REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA/RNA (5'-D(*GP*GP*AP*GP*A)-R(P*UP*GP*AP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: DDH;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL,
COMPND 7 50MM NA PHOSPHATE, 3MM EDTA;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3');
COMPND 10 CHAIN: B;
COMPND 11 SYNONYM: DDH;
COMPND 12 ENGINEERED: YES;
COMPND 13 OTHER_DETAILS: CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL,
COMPND 14 50MM NA PHOSPHATE, 3MM EDTA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: A SUBSTRATE OF RNASE H;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: A SUBSTRATE OF RNASE H
KEYWDS DOUBLE HELIX, DNA/RNA HYBRID, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
AUTHOR T.NISHIZAKI,S.IWAI,T.OHKUBO,C.KOJIMA,H.NAKAMURA,Y.KYOGOKU,E.OHTSUKA
REVDAT 4 16-FEB-22 1DRN 1 REMARK
REVDAT 3 24-FEB-09 1DRN 1 VERSN
REVDAT 2 01-APR-03 1DRN 1 JRNL
REVDAT 1 03-APR-96 1DRN 0
JRNL AUTH T.NISHIZAKI,S.IWAI,T.OHKUBO,C.KOJIMA,H.NAKAMURA,Y.KYOGOKU,
JRNL AUTH 2 E.OHTSUKA
JRNL TITL SOLUTION STRUCUTRES OF DNA DUPLEXES CONTAINING A DNA X RNA
JRNL TITL 2 HYBRID REGION, D(GG)R(AGAU)D(GAC) X D(GTCATCTCC) AND
JRNL TITL 3 D(GGAGA)R(UGAC) X D(GTCATCTCC).
JRNL REF BIOCHEMISTRY V. 35 4016 1996
JRNL REFN ISSN 0006-2960
JRNL PMID 8672435
JRNL DOI 10.1021/BI9519821
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RMSD BOND DISTANCES 0.0077 ANGSTROMS
REMARK 3 RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN
REMARK 3 REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID
REMARK 3 ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0
REMARK 3 THE STRUCTURES WAS REFINED BY A COMBINATION OF RESTRAINED
REMARK 3 MOLECULAR DYNAMICS USING THE X-PLOR (V3.1F) PROGRAM (BRUNGER
REMARK 3 1988) AND FULL RELAXATION MATRIX REFINEMENT OF THE TWO-
REMARK 3 DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRUM AT 150 MSEC.
REMARK 4
REMARK 4 1DRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000172910.
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 : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX
REMARK 210 RELAXATION
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: 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 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 G A 7 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES
REMARK 500 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG B 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DHH RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
DBREF 1DRN A 1 9 PDB 1DRN 1DRN 1 9
DBREF 1DRN B 10 18 PDB 1DRN 1DRN 10 18
SEQRES 1 A 9 DG DG DA DG DA U G A C
SEQRES 1 B 9 DG DT DC DA DT DC DT DC DC
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