HEADER DNA-RNA HYBRID 21-FEB-97 1NXR TITLE HIV-1 POLYPURINE HYBRID, R(GAGGACUG):D(CAGTCCTC), NMR, 18 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA/DNA HYBRID; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*GP*AP*GP*GP*AP*CP*UP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 SYNONYM: RNA/DNA HYBRID; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS HIV-1 POLYPURINE HYBRID, RNA/DNA HYBRID, RNASE H, REVERSE KEYWDS 2 TRANSCRIPTASE, DNA-RNA COMPLEX, DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR O.Y.FEDOROFF,Y.GE,B.R.REID REVDAT 3 23-FEB-22 1NXR 1 REMARK REVDAT 2 24-FEB-09 1NXR 1 VERSN REVDAT 1 07-JUL-97 1NXR 0 JRNL AUTH O.Y.FEDOROFF,Y.GE,B.R.REID JRNL TITL SOLUTION STRUCTURE OF R(GAGGACUG):D(CAGTCCTC) HYBRID: JRNL TITL 2 IMPLICATIONS FOR THE INITIATION OF HIV-1 (+)-STRAND JRNL TITL 3 SYNTHESIS. JRNL REF J.MOL.BIOL. V. 269 225 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9191067 JRNL DOI 10.1006/JMBI.1997.1024 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : BIOSYM TECHNOLOGIES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NXR 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_1000175408. 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 : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY 120; 180; 240; 300 MS : REMARK 210 DQF-COSY; E.COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX-750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : BIOSYM REMARK 210 METHOD USED : DISTANCE GEOMETRY, : RESTRAINED REMARK 210 MOLECULAR : DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : RMSD 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G B 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G B 3 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G B 4 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 A B 5 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 C B 6 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 G B 1 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 G B 3 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 G B 4 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 A B 5 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 C B 6 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 G B 1 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 G B 3 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 G B 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 A B 5 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 3 C B 6 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 4 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 G B 1 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 4 G B 3 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 G B 4 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 4 A B 5 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 4 C B 6 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 5 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 222 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 DC A 6 0.06 SIDE CHAIN REMARK 500 1 G B 1 0.07 SIDE CHAIN REMARK 500 1 U B 7 0.09 SIDE CHAIN REMARK 500 2 DC A 6 0.06 SIDE CHAIN REMARK 500 2 U B 7 0.10 SIDE CHAIN REMARK 500 3 DC A 6 0.06 SIDE CHAIN REMARK 500 3 G B 1 0.07 SIDE CHAIN REMARK 500 3 U B 7 0.10 SIDE CHAIN REMARK 500 4 DC A 6 0.07 SIDE CHAIN REMARK 500 4 U B 7 0.10 SIDE CHAIN REMARK 500 5 DC A 6 0.06 SIDE CHAIN REMARK 500 5 U B 7 0.11 SIDE CHAIN REMARK 500 6 DC A 6 0.06 SIDE CHAIN REMARK 500 6 G B 1 0.06 SIDE CHAIN REMARK 500 6 U B 7 0.10 SIDE CHAIN REMARK 500 7 DC A 6 0.07 SIDE CHAIN REMARK 500 7 DT A 7 0.07 SIDE CHAIN REMARK 500 7 G B 1 0.07 SIDE CHAIN REMARK 500 7 U B 7 0.10 SIDE CHAIN REMARK 500 8 U B 7 0.09 SIDE CHAIN REMARK 500 9 DC A 6 0.06 SIDE CHAIN REMARK 500 9 G B 1 0.07 SIDE CHAIN REMARK 500 9 U B 7 0.10 SIDE CHAIN REMARK 500 10 DG A 3 0.06 SIDE CHAIN REMARK 500 10 U B 7 0.10 SIDE CHAIN REMARK 500 11 DC A 6 0.07 SIDE CHAIN REMARK 500 11 G B 1 0.07 SIDE CHAIN REMARK 500 11 U B 7 0.09 SIDE CHAIN REMARK 500 12 DC A 6 0.06 SIDE CHAIN REMARK 500 12 U B 7 0.09 SIDE CHAIN REMARK 500 13 DC A 6 0.07 SIDE CHAIN REMARK 500 13 U B 7 0.09 SIDE CHAIN REMARK 500 14 DC A 6 0.07 SIDE CHAIN REMARK 500 14 U B 7 0.09 SIDE CHAIN REMARK 500 15 DC A 6 0.06 SIDE CHAIN REMARK 500 15 U B 7 0.09 SIDE CHAIN REMARK 500 16 DC A 6 0.07 SIDE CHAIN REMARK 500 16 U B 7 0.09 SIDE CHAIN REMARK 500 17 U B 7 0.09 SIDE CHAIN REMARK 500 18 DC A 6 0.06 SIDE CHAIN REMARK 500 18 U B 7 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1NXR A 1 8 PDB 1NXR 1NXR 1 8 DBREF 1NXR B 1 8 PDB 1NXR 1NXR 1 8 SEQRES 1 A 8 DC DA DG DT DC DC DT DC SEQRES 1 B 8 G A G G A C U G 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