10 20 30 40 50 60 70 80 1BN0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 31-JUL-98 1BN0
TITLE SL3 HAIRPIN FROM THE PACKAGING SIGNAL OF HIV-1, NMR, 11 TITLE 2 STRUCTURES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SL3 RNA HAIRPIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS HIV-1, PACKAGING, RNA, TETRALOOP, RIBONUCLEIC ACID, NMR
EXPDTA SOLUTION NMR
NUMMDL 11
AUTHOR L.PAPPALARDO,D.J.KERWOOD,I.PELCZER,P.N.BORER
REVDAT 2 24-FEB-09 1BN0 1 VERSN REVDAT 1 27-APR-99 1BN0 0
JRNL AUTH L.PAPPALARDO,D.J.KERWOOD,I.PELCZER,P.N.BORER JRNL TITL THREE-DIMENSIONAL FOLDING OF AN RNA HAIRPIN JRNL TITL 2 REQUIRED FOR PACKAGING HIV-1. JRNL REF J.MOL.BIOL. V. 282 801 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9743628 JRNL DOI 10.1006/JMBI.1998.2046
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AVERAGE SIXTH ROOT RESIDUAL NMR REMARK 3 INDEX = 0.07, AVERAGE RESTRAINT VIOLATION = 0.06 ANGSTROM.
REMARK 4 REMARK 4 1BN0 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) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 30MM REMARK 210 PRESSURE : NORMAL REMARK 210 SAMPLE CONTENTS : WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, DQF-COSY, H-PCOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS, DYANA, AMBER REMARK 210 METHOD USED : DISTANCE GEOMETRY, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURES WERE DETERMINED FROM 2D NOESY REMARK 210 EXPERIMENTS PERFORMED BOTH IN H2O AND D2O. THE DISTANCE REMARK 210 RESTRAINTS DETERMINED FROM MARDIGRAS WERE BASED ON INTENSITIES REMARK 210 FROM A NOESY WITH A MIXING TIME OF 300MS. DQF-COSY AND H-P REMARK 210 COSY WERE USED TO ASCERTAIN INFORMATION ABOUT THE TORSION REMARK 210 ANGLES.
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 G A 1 C3' - C2' - C1' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 7 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 1 A A 11 N9 - C1' - C2' ANGL. DEV. = 9.2 DEGREES REMARK 500 1 A A 11 N3 - C4 - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 A A 11 C6 - C5 - N7 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 13 O4' - C1' - N9 ANGL. DEV. = 16.0 DEGREES REMARK 500 1 G A 13 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 G A 13 C8 - N9 - C1' ANGL. DEV. = 8.6 DEGREES REMARK 500 1 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 A A 16 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 G A 17 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 U A 18 C5' - C4' - O4' ANGL. DEV. = 8.7 DEGREES REMARK 500 2 G A 1 C3' - C2' - C1' ANGL. DEV. = 5.6 DEGREES REMARK 500 2 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 G A 7 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 2 A A 11 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 2 G A 13 O4' - C1' - N9 ANGL. DEV. = 9.6 DEGREES REMARK 500 2 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A A 16 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 G A 17 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 U A 18 C5' - C4' - O4' ANGL. DEV. = 9.4 DEGREES REMARK 500 2 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 1 C3' - C2' - C1' ANGL. DEV. = 6.4 DEGREES REMARK 500 3 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 3 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 7 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 3 G A 9 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 A A 11 C4' - C3' - C2' ANGL. DEV. = 7.6 DEGREES REMARK 500 3 A A 11 N9 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 3 A A 11 N3 - C4 - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 A A 11 C4 - N9 - C1' ANGL. DEV. = -11.0 DEGREES REMARK 500 3 A A 11 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 3 G A 13 O4' - C1' - N9 ANGL. DEV. = 11.0 DEGREES REMARK 500 3 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 A A 16 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 17 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 3 U A 18 C5' - C4' - O4' ANGL. DEV. = 8.9 DEGREES REMARK 500 4 G A 1 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES REMARK 500 4 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 4 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 G A 7 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 4 G A 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 A A 11 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 4 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 152 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 A A 3 0.06 SIDE_CHAIN REMARK 500 1 A A 6 0.07 SIDE_CHAIN REMARK 500 1 G A 7 0.06 SIDE_CHAIN REMARK 500 1 G A 9 0.06 SIDE_CHAIN REMARK 500 1 A A 11 0.22 SIDE_CHAIN REMARK 500 1 G A 13 0.10 SIDE_CHAIN REMARK 500 1 U A 15 0.10 SIDE_CHAIN REMARK 500 1 C A 19 0.08 SIDE_CHAIN REMARK 500 1 C A 20 0.06 SIDE_CHAIN REMARK 500 2 G A 1 0.07 SIDE_CHAIN REMARK 500 2 C A 4 0.07 SIDE_CHAIN REMARK 500 2 A A 6 0.07 SIDE_CHAIN REMARK 500 2 G A 10 0.06 SIDE_CHAIN REMARK 500 2 G A 12 0.07 SIDE_CHAIN REMARK 500 2 U A 15 0.12 SIDE_CHAIN REMARK 500 2 G A 17 0.09 SIDE_CHAIN REMARK 500 2 C A 19 0.10 SIDE_CHAIN REMARK 500 3 A A 6 0.10 SIDE_CHAIN REMARK 500 3 G A 7 0.10 SIDE_CHAIN REMARK 500 3 G A 9 0.07 SIDE_CHAIN REMARK 500 3 A A 11 0.30 SIDE_CHAIN REMARK 500 3 G A 13 0.11 SIDE_CHAIN REMARK 500 3 C A 14 0.09 SIDE_CHAIN REMARK 500 3 U A 15 0.14 SIDE_CHAIN REMARK 500 3 A A 16 0.08 SIDE_CHAIN REMARK 500 3 C A 19 0.07 SIDE_CHAIN REMARK 500 3 C A 20 0.06 SIDE_CHAIN REMARK 500 4 G A 2 0.12 SIDE_CHAIN REMARK 500 4 A A 3 0.06 SIDE_CHAIN REMARK 500 4 A A 6 0.07 SIDE_CHAIN REMARK 500 4 G A 9 0.13 SIDE_CHAIN REMARK 500 4 A A 11 0.39 SIDE_CHAIN REMARK 500 4 G A 13 0.12 SIDE_CHAIN REMARK 500 4 U A 15 0.14 SIDE_CHAIN REMARK 500 4 U A 18 0.08 SIDE_CHAIN REMARK 500 4 C A 19 0.13 SIDE_CHAIN REMARK 500 5 G A 1 0.06 SIDE_CHAIN REMARK 500 5 A A 6 0.08 SIDE_CHAIN REMARK 500 5 G A 7 0.09 SIDE_CHAIN REMARK 500 5 G A 9 0.06 SIDE_CHAIN REMARK 500 5 G A 12 0.12 SIDE_CHAIN REMARK 500 5 G A 13 0.08 SIDE_CHAIN REMARK 500 5 C A 14 0.08 SIDE_CHAIN REMARK 500 5 A A 16 0.12 SIDE_CHAIN REMARK 500 5 G A 17 0.07 SIDE_CHAIN REMARK 500 5 C A 19 0.09 SIDE_CHAIN REMARK 500 5 C A 20 0.14 SIDE_CHAIN REMARK 500 6 A A 6 0.06 SIDE_CHAIN REMARK 500 6 A A 11 0.21 SIDE_CHAIN REMARK 500 6 G A 13 0.11 SIDE_CHAIN REMARK 500 6 C A 14 0.15 SIDE_CHAIN REMARK 500 6 C A 19 0.07 SIDE_CHAIN REMARK 500 6 C A 20 0.14 SIDE_CHAIN REMARK 500 7 A A 6 0.08 SIDE_CHAIN REMARK 500 7 G A 7 0.12 SIDE_CHAIN REMARK 500 7 C A 8 0.06 SIDE_CHAIN REMARK 500 7 A A 11 0.14 SIDE_CHAIN REMARK 500 7 G A 13 0.15 SIDE_CHAIN REMARK 500 7 C A 14 0.08 SIDE_CHAIN REMARK 500 7 U A 15 0.09 SIDE_CHAIN REMARK 500 7 A A 16 0.07 SIDE_CHAIN REMARK 500 7 C A 19 0.07 SIDE_CHAIN REMARK 500 7 C A 20 0.07 SIDE_CHAIN REMARK 500 8 G A 7 0.06 SIDE_CHAIN REMARK 500 8 A A 11 0.44 SIDE_CHAIN REMARK 500 8 U A 15 0.09 SIDE_CHAIN REMARK 500 8 G A 17 0.07 SIDE_CHAIN REMARK 500 8 C A 19 0.09 SIDE_CHAIN REMARK 500 8 C A 20 0.11 SIDE_CHAIN REMARK 500 9 A A 6 0.07 SIDE_CHAIN REMARK 500 9 G A 7 0.11 SIDE_CHAIN REMARK 500 9 G A 10 0.06 SIDE_CHAIN REMARK 500 9 A A 11 0.37 SIDE_CHAIN REMARK 500 9 G A 13 0.10 SIDE_CHAIN REMARK 500 9 A A 16 0.09 SIDE_CHAIN REMARK 500 10 G A 1 0.07 SIDE_CHAIN REMARK 500 10 U A 5 0.06 SIDE_CHAIN REMARK 500 10 G A 7 0.10 SIDE_CHAIN REMARK 500 10 G A 9 0.11 SIDE_CHAIN REMARK 500 10 A A 11 0.41 SIDE_CHAIN REMARK 500 10 G A 13 0.13 SIDE_CHAIN REMARK 500 10 C A 14 0.10 SIDE_CHAIN REMARK 500 10 U A 15 0.09 SIDE_CHAIN REMARK 500 11 G A 2 0.08 SIDE_CHAIN REMARK 500 11 A A 6 0.07 SIDE_CHAIN REMARK 500 11 G A 7 0.07 SIDE_CHAIN REMARK 500 11 A A 11 0.33 SIDE_CHAIN REMARK 500 11 G A 13 0.09 SIDE_CHAIN REMARK 500 11 U A 15 0.09 SIDE_CHAIN REMARK 500 11 A A 16 0.07 SIDE_CHAIN REMARK 500 11 C A 19 0.06 SIDE_CHAIN REMARK 500 11 C A 20 0.12 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1BN0 A 1 20 PDB 1BN0 1BN0 1 20
SEQRES 1 A 20 G G A C U A G C G G A G G SEQRES 2 A 20 C U A G U C C
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