Header list of 219d.pdb file
Complete list - 9 202 Bytes
HEADER DNA-RNA HYBRID 25-JUL-95 219D
TITLE DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT)
TITLE 2 (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE
TITLE 3 MOIETY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3');
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, RNA, HYBRID, PHOSPHOROTHIOATE, DNA-RNA COMPLEX, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
AUTHOR C.GONZALEZ,T.L.JAMES
REVDAT 4 09-MAR-22 219D 1 REMARK LINK
REVDAT 3 24-FEB-09 219D 1 VERSN
REVDAT 2 01-APR-03 219D 1 JRNL
REVDAT 1 15-OCT-95 219D 0
JRNL AUTH C.GONZALEZ,W.STEC,M.A.REYNOLDS,T.L.JAMES
JRNL TITL STRUCTURE AND DYNAMICS OF A DNA.RNA HYBRID DUPLEX WITH A
JRNL TITL 2 CHIRAL PHOSPHOROTHIOATE MOIETY: NMR AND MOLECULAR DYNAMICS
JRNL TITL 3 WITH CONVENTIONAL AND TIME-AVERAGED RESTRAINTS.
JRNL REF BIOCHEMISTRY V. 34 4969 1995
JRNL REFN ISSN 0006-2960
JRNL PMID 7711019
JRNL DOI 10.1021/BI00015A008
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.GONZALEZ,W.STEC,A.KOBYLANSKA,R.I.HOGREFE,M.A.REYNOLDS,
REMARK 1 AUTH 2 T.L.JAMES
REMARK 1 TITL STRUCTURAL STUDY OF A DNA(DOT)RNA HYBRID DUPLEX WITH A
REMARK 1 TITL 2 CHIRAL PHOSPHOROTHIOATE MOIETY BY NMR: EXTRACTION OF
REMARK 1 TITL 3 DISTANCE AND TORSION ANGLE CONSTRAINTS AND IMINO PROTON
REMARK 1 TITL 4 EXCHANGE RATES
REMARK 1 REF BIOCHEMISTRY V. 33 11062 1994
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : PEARLMAN,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NUMBER OF ATOMS USED IN REFINEMENT.
REMARK 3 NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411
REMARK 3 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0
REMARK 4
REMARK 4 219D 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_1000177585.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
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
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: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS
REMARK 210 MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS.
REMARK 210 TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY
REMARK 210 MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REPRESENT
REMARK 210 THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE SIXTH ROOT R-
REMARK 210 FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL NOE DATA,
REMARK 210 CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND JAMES), HAS A
REMARK 210 VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION BETWEEN
REMARK 210 EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING CONSTRAINTS
REMARK 210 IS 2.01 HZ. THIS POOR FIT OF THE COUPLING CONSTANTS IS DUE TO
REMARK 210 CONFORMATIONAL FLEXIBILITY IN THE SUGAR RING.
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 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES
REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DT A 3 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DA A 4 C3' - C2' - C1' ANGL. DEV. = 8.4 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES
REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES
REMARK 500 DA A 7 C4' - C3' - C2' ANGL. DEV. = -9.7 DEGREES
REMARK 500 DA A 7 O4' - C1' - C2' ANGL. DEV. = -10.2 DEGREES
REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES
REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 A B 13 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 U B 14 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 A B 16 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES
REMARK 500 A B 16 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 U B 17 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 A B 18 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES
REMARK 500 A B 18 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES
REMARK 500 C B 20 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
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 DG A 1 0.07 SIDE CHAIN
REMARK 500 DA A 6 0.07 SIDE CHAIN
REMARK 500 DA A 7 0.07 SIDE CHAIN
REMARK 500 C B 11 0.09 SIDE CHAIN
REMARK 500 C B 12 0.07 SIDE CHAIN
REMARK 500 A B 13 0.11 SIDE CHAIN
REMARK 500 A B 18 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 219D A 1 10 PDB 219D 219D 1 10
DBREF 219D B 11 20 PDB 219D 219D 11 20
SEQRES 1 A 10 DG DC DT DA DT DA DA PST DG DG
SEQRES 1 B 10 C C A U U A U A G C
MODRES 219D PST A 8 DT THYMIDINE-5'-THIOPHOSPHATE
HET PST A 8 20
HETNAM PST THYMIDINE-5'-THIOPHOSPHATE
FORMUL 1 PST C10 H15 N2 O7 P S
LINK O3' DA A 7 P PST A 8 1555 1555 1.60
LINK O3' PST A 8 P DG A 9 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
Complete list - 9 202 Bytes