10 20 30 40 50 60 70 80 1NXR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA-RNA HYBRID 21-FEB-97 1NXR
TITLE HIV-1 POLYPURINE HYBRID, R(GAGGACUG):D(CAGTCCTC), NMR, 18 TITLE 2 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 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) JRNL TITL 2 HYBRID: IMPLICATIONS FOR THE INITIATION OF HIV-1 JRNL TITL 3 (+)-STRAND 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER, WITH AMBER FORCE FIELD FIELD 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 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, : REMARK 210 RESTRAINED 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 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. = 4.1 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. = 6.9 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. = 6.4 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