HEADER DNA-RNA HYBRID 13-JUN-96 1GTC TITLE HUMAN IMMUNODEFICIENCY VIRUS-1 OKAZAKI FRAGMENT, DNA-RNA CHIMERA, NMR, TITLE 2 11 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*AP*GP*TP*GP*GP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3'); COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 6 ORGANISM_TAXID: 11676 KEYWDS RNA:DNA CHIMERA, RNASE H, REVERSE TRANSCRIPTASE, DNA-RNA COMPLEX, KEYWDS 2 DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR O.Y.FEDOROFF,M.SALAZAR,B.R.REID REVDAT 4 23-FEB-22 1GTC 1 REMARK REVDAT 3 24-FEB-09 1GTC 1 VERSN REVDAT 2 01-APR-03 1GTC 1 JRNL REVDAT 1 23-DEC-96 1GTC 0 JRNL AUTH O.Y.U.FEDOROFF,M.SALAZAR,B.R.REID JRNL TITL STRUCTURAL VARIATION AMONG RETROVIRAL PRIMER-DNA JUNCTIONS: JRNL TITL 2 SOLUTION STRUCTURE OF THE HIV-1 (-)-STRAND OKAZAKI FRAGMENT JRNL TITL 3 R(GCCA)D(CTGC).D(GCAGTGGC). JRNL REF BIOCHEMISTRY V. 35 11070 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8780509 JRNL DOI 10.1021/BI9607822 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SALAZAR,J.J.CHAMPOUX,B.R.REID REMARK 1 TITL SUGAR CONFORMATIONS AT HYBRID DUPLEX JUNCTIONS IN HIV-1 AND REMARK 1 TITL 2 OKAZAKI FRAGMENTS REMARK 1 REF BIOCHEMISTRY V. 32 739 1993 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 : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GTC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173704. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 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 : NOESY; DQF-COSY; E.COSY; H-P REMARK 210 HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : HOME-BUILD; DROBNY; GLADDEN REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DISCOVER, DG-II, BIRDER REMARK 210 METHOD USED : DISTANCE GEOMETRY, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 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 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C B 2 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 C B 3 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 C B 2 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 2 C B 2 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DC B 5 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 C B 2 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 3 C B 2 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 3 DC B 5 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 3 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DC B 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DC A 8 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 G B 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 C B 2 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 4 C B 2 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 4 C B 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DC B 5 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 4 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DC B 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 5 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 5 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 125 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 B 1 0.06 SIDE CHAIN REMARK 500 1 C B 3 0.07 SIDE CHAIN REMARK 500 1 A B 4 0.08 SIDE CHAIN REMARK 500 2 C B 2 0.09 SIDE CHAIN REMARK 500 2 A B 4 0.06 SIDE CHAIN REMARK 500 3 C B 2 0.08 SIDE CHAIN REMARK 500 3 A B 4 0.06 SIDE CHAIN REMARK 500 4 C B 2 0.08 SIDE CHAIN REMARK 500 4 A B 4 0.06 SIDE CHAIN REMARK 500 5 C B 2 0.09 SIDE CHAIN REMARK 500 5 A B 4 0.05 SIDE CHAIN REMARK 500 6 C B 2 0.09 SIDE CHAIN REMARK 500 6 A B 4 0.06 SIDE CHAIN REMARK 500 7 C B 2 0.09 SIDE CHAIN REMARK 500 7 A B 4 0.05 SIDE CHAIN REMARK 500 8 C B 2 0.08 SIDE CHAIN REMARK 500 8 A B 4 0.05 SIDE CHAIN REMARK 500 9 C B 2 0.09 SIDE CHAIN REMARK 500 9 A B 4 0.06 SIDE CHAIN REMARK 500 10 C B 2 0.08 SIDE CHAIN REMARK 500 10 A B 4 0.06 SIDE CHAIN REMARK 500 11 C B 2 0.07 SIDE CHAIN REMARK 500 11 A B 4 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1GTC A 1 8 PDB 1GTC 1GTC 1 8 DBREF 1GTC B 1 8 PDB 1GTC 1GTC 1 8 SEQRES 1 A 8 DG DC DA DG DT DG DG DC 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