HEADER RNA 12-JAN-04 1S34 TITLE SOLUTION STRUCTURE OF RESIDUES 907-929 FROM ROUS SARCOMA TITLE 2 VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*GP*GP*AP*GP*UP*GP*GP*UP*UP*UP*GP*UP*AP*UP*CP*CP*UP COMPND 4 *UP*CP*CP*C)-3'; COMPND 5 CHAIN: A; COMPND 6 FRAGMENT: PSEUDO 5'-SPLICE SITE; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION KEYWDS STEM-LOOP, TETRALOOP, BULGE, RNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.CABELLO-VILLEGAS,K.E.GILES,A.M.SOTO,P.YU,K.L.BEEMON, AUTHOR 2 Y.X.WANG REVDAT 2 24-FEB-09 1S34 1 VERSN REVDAT 1 31-AUG-04 1S34 0 JRNL AUTH J.CABELLO-VILLEGAS,K.E.GILES,A.M.SOTO,P.YU, JRNL AUTH 2 A.MOUGIN,K.L.BEEMON,Y.X.WANG JRNL TITL SOLUTION STRUCTURE OF THE PSEUDO-5' SPLICE SITE OF JRNL TITL 2 A RETROVIRAL SPLICING SUPPRESSOR. JRNL REF RNA V. 10 1388 2004 JRNL REFN ISSN 1355-8382 JRNL PMID 15317975 JRNL DOI 10.1261/RNA.7020804 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.0.6 REMARK 3 AUTHORS : C.D. SCHWIETERS, J.J. KUSZEWSKI, N. TJANDRA, REMARK 3 AND G.M. CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DELPHIC TORSION ANGLE POTENTIAL WAS REMARK 3 USED FOR THE WHOLE MOLECULE. THE BASE POSITION POTENTIAL WAS REMARK 3 EXCLUDED FOR RESIDUES 913, AND 917 TO 920. PROTOCOL FROM CLORE REMARK 3 AND KUSZEWSKI (J AM CHEM SOC. 2003. 125(6):1518-25) REMARK 4 REMARK 4 1S34 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-04. REMARK 100 THE RCSB ID CODE IS RCSB021306. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 25MM NACL, 10 MM SODIUM REMARK 210 PHOSPHATE; 25MM NACL, 10 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM 23 MER RNA (NRS23); 1 MM REMARK 210 NRS23 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_13C-SEPARATED_ REMARK 210 NOESY, DQF-COSY, HNN-COSY, HCP REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX, INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER, VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, NMRPIPE 4.1, REMARK 210 NMRDRAW 4.1, NMRVIEW 5.0.4, X- REMARK 210 PLOR NIH 2.0.6 REMARK 210 METHOD USED : SIMULATED ANNEALING. REMARK 210 REFINEMENT USING TORSION ANGLE REMARK 210 DYNAMICS AND THE DELPHIC REMARK 210 DATABASE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: RDC RESTRAINTS WERE OBTAINED FOR THE BASE ONE BOND H-C REMARK 210 AND H-N USING HSQC EXPERIMENTS. RDC RESTRAINTS FOR THE RIBOSE REMARK 210 WERE OBTAINED FROM MEASUREMENTS ON AN RELAY HCCH-COSY REMARK 210 (VALLURUPALLI AND MOORE, J BIOMOL NMR. 2002. 24(1):63-6). REMARK 210 ANISOTROPIC CONDITIONS WERE ~20 MG/ML PF1 PHAGE. 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 3 U A 917 C4' U A 917 C3' 0.097 REMARK 500 4 G A 919 C4' G A 919 C3' -0.074 REMARK 500 7 U A 918 C4' U A 918 C3' -0.094 REMARK 500 11 U A 918 C4' U A 918 C3' -0.077 REMARK 500 11 U A 920 C4' U A 920 C3' -0.091 REMARK 500 12 U A 918 C4' U A 918 C3' -0.078 REMARK 500 13 G A 909 C4' G A 909 C3' 0.078 REMARK 500 14 U A 918 C4' U A 918 C3' -0.068 REMARK 500 REMARK 500 REMARK: NULL 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 919 O4' - C4' - C3' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 U A 918 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES REMARK 500 3 U A 917 C5' - C4' - C3' ANGL. DEV. = -10.6 DEGREES REMARK 500 3 G A 919 O4' - C4' - C3' ANGL. DEV. = 6.7 DEGREES REMARK 500 4 U A 918 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES REMARK 500 5 G A 919 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 6 U A 918 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES REMARK 500 7 U A 918 O4' - C4' - C3' ANGL. DEV. = 6.0 DEGREES REMARK 500 7 G A 919 O4' - C4' - C3' ANGL. DEV. = 6.0 DEGREES REMARK 500 11 U A 918 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES REMARK 500 13 U A 918 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES REMARK 500 14 U A 918 O4' - C4' - C3' ANGL. DEV. = 5.8 DEGREES REMARK 500 14 G A 919 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S2F RELATED DB: PDB REMARK 900 MINIMZED AVERAGE STRUCTURE FROM THESE LOWEST ENERGY REMARK 900 STRUCTURES. DBREF 1S34 A 907 929 PDB 1S34 1S34 907 929 SEQRES 1 A 23 G G G G A G U G G U U U G SEQRES 2 A 23 U A U C C U U C 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 125 0 0 0 0 0 0 6 0 0 0 2 END