Header list of 1c2q.pdb file
Complete list - 16 202 Bytes
HEADER DNA-RNA HYBRID 26-JUL-99 1C2Q
TITLE SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC
TITLE 2 THYMIDINE AND POLARITY REVERSALS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: T5 IS ALPHAT ANOMERIC;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 5'-R(GAGCACCAU)-3';
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHETIC;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: SYNTHETIC
KEYWDS DNA/RNA HYBRID, ALPHAT-ANOMERIC THYMIDINE, 3'-3'/5'-5' PHOSPHODIESTER
KEYWDS 2 LINKAGES, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.W.GERMANN,J.M.ARAMINI
REVDAT 4 16-FEB-22 1C2Q 1 REMARK LINK
REVDAT 3 24-FEB-09 1C2Q 1 VERSN
REVDAT 2 01-APR-03 1C2Q 1 JRNL
REVDAT 1 29-NOV-99 1C2Q 0
JRNL AUTH J.M.ARAMINI,M.W.GERMANN
JRNL TITL SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN
JRNL TITL 2 ALPHA-ANOMERIC THYMIDINE AND POLARITY REVERSALS:
JRNL TITL 3 D(ATGG-3'-3'-ALPHAT-5'-5'-GCTC). R(GAGCACCAU).
JRNL REF BIOCHEMISTRY V. 38 15448 1999
JRNL REFN ISSN 0006-2960
JRNL PMID 10569927
JRNL DOI 10.1021/BI9915418
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.M.ARAMINI,A.MUJEEB,M.W.GERMANN
REMARK 1 TITL NMR SOLUTION STRUCTURES OF
REMARK 1 TITL 2 [D(GCGAAT-3'-3'-(ALPHA-T)-5'-5'-CGC)2] AND ITS UNMODIFIED
REMARK 1 TITL 3 CONTROL
REMARK 1 REF NUCLEIC ACIDS RES. V. 26 5644 1998
REMARK 1 REFN ISSN 0305-1048
REMARK 1 DOI 10.1093/NAR/26.24.5644
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : UXNMR 2.1, AMBER 4.1
REMARK 3 AUTHORS : BRUKER (UXNMR), PEARLMAN ET AL., 1995 (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF
REMARK 3 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE
REMARK 3 RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45
REMARK 3 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM
REMARK 3 PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE
REMARK 3 RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE
REMARK 3 RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY
REMARK 3 COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES,
REMARK 3 FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE
REMARK 3 CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN
REMARK 3 AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION.
REMARK 3 ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE
REMARK 3 DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED
REMARK 3 INTERACTIONS.
REMARK 4
REMARK 4 1C2Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-99.
REMARK 100 THE DEPOSITION ID IS D_1000009406.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 298
REMARK 210 PH : 6.6; 6.7
REMARK 210 IONIC STRENGTH : NULL; NULL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.89 MM HYBRID, 50 MM NACL, 10
REMARK 210 MM PHOSPHATE BUFFER, 0.5 MM EDTA,
REMARK 210 PH* 6.6, D2O; 0.89 MM HYBRID,
REMARK 210 50 MM NACL, 10 MM PHOSPHATE
REMARK 210 BUFFER, 0.5 MM EDTA, PH 6.7, 90%
REMARK 210 H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 31P-1H
REMARK 210 CORRELATION SPECTROSCOPY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS 3.2, CORMA 5.2, SPARKY
REMARK 210 3.33, SPHINX/LINSHA, CURVES 5.1,
REMARK 210 AMBER 4.1
REMARK 210 METHOD USED : SIMULATED ANNEALING/MOLECULAR
REMARK 210 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 : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR NMR 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 DA A 1 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 T3P A 5 O3' - P - O5' ANGL. DEV. = 53.2 DEGREES
REMARK 500 DG A 6 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES
REMARK 500 DG A 6 C3' - C2' - C1' ANGL. DEV. = 8.2 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC A 7 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES
REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 G B 10 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 A B 11 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 A B 11 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 G B 12 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES
REMARK 500 C B 13 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 C B 15 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 C B 16 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES
REMARK 500 U B 18 O4' - C1' - N1 ANGL. DEV. = 4.8 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 6 0.07 SIDE CHAIN
REMARK 500 A B 11 0.06 SIDE CHAIN
REMARK 500 A B 14 0.10 SIDE CHAIN
REMARK 500 A B 17 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1BX5 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF A SELF-COMPLEMENTARY DNA DUPLEX CONTAINING
REMARK 900 THE SAME MODIFICATIONS (1 ALPHA-ANOMERIC THYMIDINE AND FLANKING 3'-
REMARK 900 3' AND 5'-5' PHOSPHODIESTER LINKAGES PER STRAND)
DBREF 1C2Q A 1 9 PDB 1C2Q 1C2Q 1 9
DBREF 1C2Q B 10 18 PDB 1C2Q 1C2Q 10 18
SEQRES 1 A 9 DA DT DG DG T3P DG DC DT DC
SEQRES 1 B 9 G A G C A C C A U
MODRES 1C2Q T3P A 5 DT THYMIDINE-3'-PHOSPHATE
HET T3P A 5 32
HETNAM T3P THYMIDINE-3'-PHOSPHATE
HETSYN T3P ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE
FORMUL 1 T3P C10 H15 N2 O8 P
LINK O3' DG A 4 P T3P A 5 1555 1555 1.61
LINK O5' T3P A 5 P DG A 6 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 - 16 202 Bytes