HEADER RNA 20-MAR-03 1OSW TITLE THE STEM OF SL1 RNA IN HIV-1: STRUCTURE AND NUCLEOCAPSID TITLE 2 PROTEIN BINDING FOR A 1X3 INTERNAL LOOP CAVEAT 1OSW CHIRALITY ERRORS EXIST IN SOME MODELS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*AP*GP*GP*CP*GP*CP*UP*AP*CP*GP*GP*CP*GP*AP*GP*GP*CP COMPND 4 *UP*CP*CP*A)-3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: STEM OF SL1 RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA SEQUENCE OBTAINED FROM DHARMACON KEYWDS RNA EXPDTA SOLUTION NMR NUMMDL 23 AUTHOR Y.YUAN,D.J.KERWOOD,A.C.PAOLETTI,M.F.SHUBSDA,P.N.BORER REVDAT 2 24-FEB-09 1OSW 1 VERSN REVDAT 1 20-MAY-03 1OSW 0 JRNL AUTH Y.YUAN,D.J.KERWOOD,A.C.PAOLETTI,M.F.SHUBSDA, JRNL AUTH 2 P.N.BORER JRNL TITL STEM OF SL1 RNA IN HIV-1: STRUCTURE AND JRNL TITL 2 NUCLEOCAPSID PROTEIN BINDING FOR A 1X3 INTERNAL JRNL TITL 3 LOOP JRNL REF BIOCHEMISTRY V. 42 5259 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12731867 JRNL DOI 10.1021/BI034084A REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : UNIVERSITY OF CALIFORNIA, SAN FRANCISCO REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OSW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-03. REMARK 100 THE RCSB ID CODE IS RCSB018635. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 278 REMARK 210 PH : 6.3; 5.5 REMARK 210 IONIC STRENGTH : 25 MM NACL; 25 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM SL1I RNA; 25MM NACL, 5MM REMARK 210 SODIUM PHOSPHATE, 0.1MM EDTA, REMARK 210 0.01% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, HP-COSY, REMARK 210 H-C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRZ/TRIAD 6.1, REMARK 210 MARDIGRAS 3.2, DYANA 1.5 REMARK 210 METHOD USED : DYANA FOLLOWED BY MOLECULAR REMARK 210 DYNAMICS USING AMBER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY,TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 17 REMARK 210 REMARK 210 REMARK: STRUCTURES WERE DETERMINED USING 2D NOESY AT DIFFERENT REMARK 210 TEMPERATURES AND MIXING TIMES. THE LAST RESIDUE, A23, WAS REMARK 210 ELIMINATED FROM THE PDB FILE DUE TO AMBIGUITY IN ORIENTATION. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-23 REMARK 465 RES C SSSEQI REMARK 465 A A 23 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 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 C A 14 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 18 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 4 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 6 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 7 G A 12 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 7 C A 14 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 7 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 8 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 8 C A 21 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 8 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 9 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 10 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 G A 17 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 11 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 13 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 13 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 14 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 15 G A 18 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 15 G A 18 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 16 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 16 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 16 C A 19 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 16 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 17 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 17 G A 12 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 18 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 18 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 18 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 19 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 19 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 19 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 20 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 20 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 20 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 20 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 61 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 12 0.07 SIDE_CHAIN REMARK 500 2 G A 7 0.06 SIDE_CHAIN REMARK 500 2 C A 14 0.07 SIDE_CHAIN REMARK 500 3 G A 4 0.07 SIDE_CHAIN REMARK 500 3 G A 18 0.07 SIDE_CHAIN REMARK 500 4 U A 9 0.07 SIDE_CHAIN REMARK 500 4 G A 18 0.08 SIDE_CHAIN REMARK 500 4 U A 20 0.06 SIDE_CHAIN REMARK 500 4 C A 21 0.07 SIDE_CHAIN REMARK 500 5 C A 6 0.08 SIDE_CHAIN REMARK 500 5 G A 18 0.06 SIDE_CHAIN REMARK 500 6 G A 12 0.06 SIDE_CHAIN REMARK 500 6 G A 13 0.08 SIDE_CHAIN REMARK 500 7 G A 7 0.06 SIDE_CHAIN REMARK 500 7 U A 9 0.07 SIDE_CHAIN REMARK 500 7 G A 12 0.06 SIDE_CHAIN REMARK 500 7 C A 19 0.10 SIDE_CHAIN REMARK 500 7 U A 20 0.07 SIDE_CHAIN REMARK 500 8 U A 9 0.10 SIDE_CHAIN REMARK 500 8 C A 21 0.06 SIDE_CHAIN REMARK 500 9 U A 9 0.08 SIDE_CHAIN REMARK 500 9 G A 18 0.09 SIDE_CHAIN REMARK 500 10 U A 9 0.07 SIDE_CHAIN REMARK 500 11 G A 1 0.06 SIDE_CHAIN REMARK 500 11 G A 18 0.08 SIDE_CHAIN REMARK 500 13 U A 9 0.09 SIDE_CHAIN REMARK 500 13 G A 13 0.08 SIDE_CHAIN REMARK 500 13 G A 18 0.05 SIDE_CHAIN REMARK 500 13 U A 20 0.06 SIDE_CHAIN REMARK 500 14 G A 4 0.06 SIDE_CHAIN REMARK 500 14 U A 9 0.08 SIDE_CHAIN REMARK 500 14 G A 12 0.06 SIDE_CHAIN REMARK 500 14 G A 18 0.05 SIDE_CHAIN REMARK 500 15 G A 7 0.05 SIDE_CHAIN REMARK 500 15 G A 12 0.05 SIDE_CHAIN REMARK 500 16 C A 11 0.09 SIDE_CHAIN REMARK 500 17 G A 7 0.06 SIDE_CHAIN REMARK 500 17 C A 19 0.08 SIDE_CHAIN REMARK 500 17 C A 21 0.08 SIDE_CHAIN REMARK 500 18 C A 11 0.07 SIDE_CHAIN REMARK 500 18 C A 14 0.07 SIDE_CHAIN REMARK 500 19 G A 17 0.06 SIDE_CHAIN REMARK 500 19 G A 18 0.06 SIDE_CHAIN REMARK 500 20 G A 7 0.06 SIDE_CHAIN REMARK 500 20 C A 19 0.09 SIDE_CHAIN REMARK 500 21 G A 7 0.06 SIDE_CHAIN REMARK 500 21 G A 12 0.06 SIDE_CHAIN REMARK 500 21 A A 16 0.06 SIDE_CHAIN REMARK 500 22 G A 5 0.05 SIDE_CHAIN REMARK 500 22 G A 7 0.06 SIDE_CHAIN REMARK 500 22 U A 9 0.09 SIDE_CHAIN REMARK 500 22 G A 12 0.08 SIDE_CHAIN REMARK 500 22 G A 13 0.05 SIDE_CHAIN REMARK 500 22 G A 18 0.07 SIDE_CHAIN REMARK 500 22 C A 22 0.09 SIDE_CHAIN REMARK 500 23 C A 14 0.10 SIDE_CHAIN REMARK 500 23 G A 18 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1OSW A 1 23 PDB 1OSW 1OSW 1 23 SEQRES 1 A 23 G G A G G C G C U A C G G SEQRES 2 A 23 C G A G G C U C C A 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 206 0 0 0 0 0 0 6 0 0 0 2 END