Header list of 1byx.pdb file
Complete list - 16 20 Bytes
HEADER DNA-RNA HYBRID 20-OCT-98 1BYX
TITLE CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-
TITLE 2 DNA JUNCTION FORMED DURING INITIATION OF HIV-1 REVERSE TRANSCRIPTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3');
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES;
COMPND 9 OTHER_DETAILS: CHIMERIC HYBRID RNA/RNA-DNA DUPLEX
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THE RNA:RNA-DNA CHIMERIC HYBRID DUPLEX WAS CHEMICALLY
SOURCE 4 SYNTHESIZED FROM THE HUMAN IMMUNODIFICIENCY VIRUS TYPE 1 (HIV-1).
SOURCE 5 THE DUPLEX IS FORMED DURING THE INITIATION OF (-)DNA STRAND
SOURCE 6 SYNTHESIS IN HIV-1 REPLICATION.;
SOURCE 7 MOL_ID: 2;
SOURCE 8 SYNTHETIC: YES
KEYWDS RNA:RNA-DNA CHIMERIC HYBRID, RNASE H, REVERSE TRANSCRIPTASE, DNA-RNA
KEYWDS 2 COMPLEX, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR T.SZYPERSKI,M.GOETTE,M.BILLETER,E.PEROLA,L.CELLAI
REVDAT 4 16-FEB-22 1BYX 1 REMARK
REVDAT 3 24-FEB-09 1BYX 1 VERSN
REVDAT 2 01-APR-03 1BYX 1 JRNL
REVDAT 1 20-OCT-99 1BYX 0
JRNL AUTH T.SZYPERSKI,M.GOTTE,M.BILLETER,E.PEROLA,L.CELLAI,H.HEUMANN,
JRNL AUTH 2 K.WUTHRICH
JRNL TITL NMR STRUCTURE OF THE CHIMERIC HYBRID DUPLEX
JRNL TITL 2 R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-DNA JUNCTION
JRNL TITL 3 FORMED DURING INITIATION OF HIV-1 REVERSE TRANSCRIPTION.
JRNL REF J.BIOMOL.NMR V. 13 343 1999
JRNL REFN ISSN 0925-2738
JRNL PMID 10353196
JRNL DOI 10.1023/A:1008350604637
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA
REMARK 3 AUTHORS : GUNTERT,WUTHRICH
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS ARE DESCRIBED IN THE
REMARK 3 JRNL CITATION ABOVE
REMARK 4
REMARK 4 1BYX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-99.
REMARK 100 THE DEPOSITION ID IS D_1000007043.
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 : 1 ATM
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; E H-P
REMARK 210 HETCOR; H-C COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : AMX; UNITY
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DYANA
REMARK 210 METHOD USED : DISTANCE GEOMETRY
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : DYANA TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK:
REMARK 210 THE 20 STRUCTURES ARE ENERGY-MINIMIZED WITH THE AMBER FORCE FIELD
REMARK 210 USING THE
REMARK 210 PROGRAM OPAL
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OP2 G A 7 HO3' C A 8 1.56
REMARK 500
REMARK 500 REMARK: NULL
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 C A 2 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 G B 101 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 C B 102 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 C B 103 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DC B 105 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 1 DT B 106 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DG B 107 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DC B 108 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 C A 2 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 C A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 C B 103 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 2 DC B 105 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 2 DT B 106 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DG B 107 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DC B 108 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 3 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 3 G A 4 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 3 G A 7 O4' - C1' - N9 ANGL. DEV. = 8.1 DEGREES
REMARK 500 3 C B 102 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 3 C B 103 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 3 DC B 105 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DT B 106 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 3 DG B 107 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 4 G A 1 N3 - C2 - N2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 4 C A 2 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 4 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 4 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 4 G A 6 C5' - C4' - O4' ANGL. DEV. = 5.8 DEGREES
REMARK 500 4 C B 102 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 4 DC B 105 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 4 DT B 106 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 4 DG B 107 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 4 DC B 108 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 4 DC B 108 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 5 C A 2 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 5 A A 3 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES
REMARK 500 5 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 5 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 5 C B 102 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 5 C B 103 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 5 DC B 105 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES
REMARK 500 5 DC B 105 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 5 DT B 106 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 5 DT B 106 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 5 DG B 107 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 206 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 4 0.07 SIDE CHAIN
REMARK 500 1 U A 5 0.08 SIDE CHAIN
REMARK 500 1 G A 7 0.08 SIDE CHAIN
REMARK 500 1 G B 101 0.06 SIDE CHAIN
REMARK 500 1 C B 102 0.08 SIDE CHAIN
REMARK 500 1 DG B 107 0.10 SIDE CHAIN
REMARK 500 2 G A 4 0.10 SIDE CHAIN
REMARK 500 2 U A 5 0.11 SIDE CHAIN
REMARK 500 2 G A 7 0.11 SIDE CHAIN
REMARK 500 2 C B 103 0.06 SIDE CHAIN
REMARK 500 2 A B 104 0.09 SIDE CHAIN
REMARK 500 3 A A 3 0.11 SIDE CHAIN
REMARK 500 3 G A 4 0.09 SIDE CHAIN
REMARK 500 3 U A 5 0.09 SIDE CHAIN
REMARK 500 3 C A 8 0.07 SIDE CHAIN
REMARK 500 3 C B 102 0.09 SIDE CHAIN
REMARK 500 3 A B 104 0.09 SIDE CHAIN
REMARK 500 4 C A 2 0.07 SIDE CHAIN
REMARK 500 4 G A 4 0.11 SIDE CHAIN
REMARK 500 4 G B 101 0.05 SIDE CHAIN
REMARK 500 4 C B 102 0.09 SIDE CHAIN
REMARK 500 4 DT B 106 0.10 SIDE CHAIN
REMARK 500 5 G A 1 0.07 SIDE CHAIN
REMARK 500 5 G A 4 0.13 SIDE CHAIN
REMARK 500 5 U A 5 0.08 SIDE CHAIN
REMARK 500 5 C A 8 0.08 SIDE CHAIN
REMARK 500 5 G B 101 0.11 SIDE CHAIN
REMARK 500 5 A B 104 0.07 SIDE CHAIN
REMARK 500 5 DC B 105 0.10 SIDE CHAIN
REMARK 500 5 DT B 106 0.07 SIDE CHAIN
REMARK 500 5 DC B 108 0.10 SIDE CHAIN
REMARK 500 6 G A 1 0.07 SIDE CHAIN
REMARK 500 6 G A 4 0.15 SIDE CHAIN
REMARK 500 6 U A 5 0.11 SIDE CHAIN
REMARK 500 6 G B 101 0.06 SIDE CHAIN
REMARK 500 6 C B 103 0.14 SIDE CHAIN
REMARK 500 6 A B 104 0.07 SIDE CHAIN
REMARK 500 7 C A 2 0.19 SIDE CHAIN
REMARK 500 7 G A 4 0.07 SIDE CHAIN
REMARK 500 7 U A 5 0.08 SIDE CHAIN
REMARK 500 7 G B 101 0.14 SIDE CHAIN
REMARK 500 7 C B 102 0.08 SIDE CHAIN
REMARK 500 7 DC B 105 0.07 SIDE CHAIN
REMARK 500 7 DT B 106 0.10 SIDE CHAIN
REMARK 500 7 DG B 107 0.09 SIDE CHAIN
REMARK 500 8 G A 1 0.07 SIDE CHAIN
REMARK 500 8 C A 2 0.10 SIDE CHAIN
REMARK 500 8 G A 4 0.12 SIDE CHAIN
REMARK 500 8 U A 5 0.08 SIDE CHAIN
REMARK 500 8 A B 104 0.09 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 142 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1BYX A 1 8 PDB 1BYX 1BYX 1 8
DBREF 1BYX B 101 108 PDB 1BYX 1BYX 101 108
SEQRES 1 A 8 G C A G U G G C
SEQRES 1 B 8 G C C A DC DT DG 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
MODEL 1
Complete list - 16 20 Bytes