Header list of 1oo7.pdb file
Complete list - 28 20 Bytes
HEADER DNA-RNA HYBRID 03-MAR-03 1OO7
TITLE DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-
TITLE 2 RICH RNA STRAND, NMR, 4 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU)
COMPND 7 P*(PDU)P*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.RNA HYBRID, PURINE/PYRIMIDINE-RICH STRANDS, ANTISENSE, DNA-RNA
KEYWDS 2 COMPLEX, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
NUMMDL 4
MDLTYP MINIMIZED AVERAGE
AUTHOR J.I.GYI,D.GAO,G.L.CONN,J.O.TRENT,T.BROWN,A.N.LANE
REVDAT 4 28-JUL-21 1OO7 1 COMPND REMARK SEQRES FORMUL
REVDAT 4 2 1 LINK ATOM
REVDAT 3 24-FEB-09 1OO7 1 VERSN
REVDAT 2 25-NOV-03 1OO7 3 ATOM
REVDAT 1 11-NOV-03 1OO7 0
JRNL AUTH J.I.GYI,D.GAO,G.L.CONN,J.O.TRENT,T.BROWN,A.N.LANE
JRNL TITL THE SOLUTION STRUCTURE OF A DNA*RNA DUPLEX CONTAINING
JRNL TITL 2 5-PROPYNYL U AND C; COMPARISON WITH 5-ME MODIFICATIONS
JRNL REF NUCLEIC ACIDS RES. V. 31 2683 2003
JRNL REFN ISSN 0305-1048
JRNL PMID 12736318
JRNL DOI 10.1093/NAR/GKG356
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.I.GYI,A.N.LANE,G.L.CONN,T.BROWN
REMARK 1 TITL SOLUTION STRUCTURES OF DNA.RNA HYBRIDS WITH PURINE-RICH AND
REMARK 1 TITL 2 PYRIMIDINE-RICH STRANDS: COMPARISON WITH THE HOMOLOGOUS DNA
REMARK 1 TITL 3 AND RNA DUPLEXES
REMARK 1 REF BIOCHEMISTRY V. 37 73 1998
REMARK 1 REFN ISSN 0006-2960
REMARK 1 DOI 10.1021/BI9719713
REMARK 1 REFERENCE 2
REMARK 1 AUTH J.I.GYI,G.L.CONN,A.N.LANE,T.BROWN
REMARK 1 TITL COMPARISON OF THE THERMODYNAMIC STABILITIES AND SOLUTION
REMARK 1 TITL 2 CONFORMATIONS OF DNA.RNA HYBRIDS CONTAINING PURINE-RICH AND
REMARK 1 TITL 3 PYRIMIDINE-RICH STRANDS WITH DNA AND RNA DUPLEXES
REMARK 1 REF BIOCHEMISTRY V. 35 12538 1996
REMARK 1 REFN ISSN 0006-2960
REMARK 1 DOI 10.1021/BI960948Z
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 7.0
REMARK 3 AUTHORS : CORNELL, W.D., ET AL.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE CONSTRAINTS FOR GLYCOSIDIC
REMARK 3 TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES
REMARK 3 AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP
REMARK 3 CURVES AND COUPLING CONSTANTS BY A LEAST-SQUARES/GRID SEARCH
REMARK 3 METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). TEN
REMARK 3 DIFFERENT SETS OF UNIQUE RESTRAINTS GENERATED 10 STRUCTURES, THE
REMARK 3 AVERAGE OF WHICH SATISFIED THE EXPERIMENTALLY DERIVED FRACTION
REMARK 3 OF SOUTH STATE SUGARS BETTER THAN STRUCTURES GENERATED FROM A
REMARK 3 SINGLE SET OF RESTRAINTS. INTERNUCLEOTIDE DISTANCE CONSTRAINTS
REMARK 3 CALCULATED FROM NOE-BUILD-UP CURVES. STRUCTURES CALCULATED BY
REMARK 3 SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN
REMARK 3 AMBER FORCE FIELD AND A DISTANCE DIELECTRIC CONSTANT.
REMARK 4
REMARK 4 1OO7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-03.
REMARK 100 THE DEPOSITION ID IS D_1000018494.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 100 MM KCL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 95.0, NUCFIT, PFIT
REMARK 210 METHOD USED : MULTIPLE STARTING CONFORMATIONS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 4
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED FROM 2D HOMONUCLEAR NMR
REMARK 210 EXPERIMENTS USING UNLABELLED SAMPLE
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 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 G A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 4 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 G A 4 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 A A 5 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 G A 6 N3 - C2 - N2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 8 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 G A 9 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DG B 1 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 2 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 2 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 2 G A 4 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 2 G A 4 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 2 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 A A 5 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES
REMARK 500 2 G A 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 2 G A 6 N3 - C2 - N2 ANGL. DEV. = -5.0 DEGREES
REMARK 500 2 G A 6 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 A A 7 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 A A 8 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES
REMARK 500 2 G A 9 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 G A 9 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 2 G A 9 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 2 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 2 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 2 DG B 1 N3 - C2 - N2 ANGL. DEV. = -5.0 DEGREES
REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.0 DEGREES
REMARK 500 3 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 3 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 A A 3 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 3 G A 4 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 3 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 3 G A 6 N3 - C2 - N2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 3 G A 6 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 3 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 A A 7 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 77 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 G A 1 0.06 SIDE CHAIN
REMARK 500 2 DG B 1 0.06 SIDE CHAIN
REMARK 500 4 DG B 1 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DRR RELATED DB: PDB
REMARK 900 DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH DNA STRAND, NMR, 10
REMARK 900 STRUCTURES
REMARK 900 RELATED ID: 1RRD RELATED DB: PDB
REMARK 900 DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10
REMARK 900 STRUCTURES
DBREF 1OO7 A 1 10 PDB 1OO7 1OO7 1 10
DBREF 1OO7 B 1 10 PDB 1OO7 1OO7 1 10
SEQRES 1 A 10 G A A G A G A A G C
SEQRES 1 B 10 DG 5PC PDU PDU 5PC PDU 5PC PDU PDU DC
MODRES 1OO7 5PC B 2 DC
MODRES 1OO7 PDU B 3 DU
MODRES 1OO7 PDU B 4 DU
MODRES 1OO7 5PC B 5 DC
MODRES 1OO7 PDU B 6 DU
MODRES 1OO7 5PC B 7 DC
MODRES 1OO7 PDU B 8 DU
MODRES 1OO7 PDU B 9 DU
HET 5PC B 2 35
HET PDU B 3 34
HET PDU B 4 34
HET 5PC B 5 35
HET PDU B 6 34
HET 5PC B 7 35
HET PDU B 8 34
HET PDU B 9 34
HETNAM 5PC 5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
HETNAM PDU 5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE
FORMUL 2 5PC 3(C12 H16 N3 O7 P)
FORMUL 2 PDU 5(C12 H15 N2 O8 P)
LINK O3' DG B 1 P 5PC B 2 1555 1555 1.61
LINK O3' 5PC B 2 P PDU B 3 1555 1555 1.60
LINK O3' PDU B 3 P PDU B 4 1555 1555 1.61
LINK O3' PDU B 4 P 5PC B 5 1555 1555 1.61
LINK O3' 5PC B 5 P PDU B 6 1555 1555 1.60
LINK O3' PDU B 6 P 5PC B 7 1555 1555 1.61
LINK O3' 5PC B 7 P PDU B 8 1555 1555 1.60
LINK O3' PDU B 8 P PDU B 9 1555 1555 1.61
LINK O3' PDU B 9 P DC B 10 1555 1555 1.61
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 - 28 20 Bytes