HEADER RNA 08-JAN-04 1S2F TITLE AVERAGE SOLUTION STRUCTURE OF A PSEUDO-5'-SPLICE SITE FROM THE TITLE 2 NEGATIVE REGULATOR OF SPLICING OF ROUS SARCOMA VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*GP*GP*AP*GP*UP*GP*GP*UP*UP*UP*GP*UP*AP*UP*CP*CP COMPND 3 *UP*UP*CP*CP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PSEUDO 5'-SPLICE SITE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION KEYWDS NRS, U1 SNRNP BINDING SITE, 5' SPLICE SITE, RNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.CABELLO-VILLEGAS,K.E.GILES,A.M.SOTO,P.YU,K.L.BEEMON,Y.X.WANG REVDAT 3 02-MAR-22 1S2F 1 REMARK REVDAT 2 24-FEB-09 1S2F 1 VERSN REVDAT 1 31-AUG-04 1S2F 0 JRNL AUTH J.CABELLO-VILLEGAS,K.E.GILES,A.M.SOTO,P.YU,A.MOUGIN, JRNL AUTH 2 K.L.BEEMON,Y.X.WANG JRNL TITL SOLUTION STRUCTURE OF THE PSEUDO-5' SPLICE SITE OF A JRNL TITL 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH XPLOR-NIH-2.0.6 REMARK 3 AUTHORS : C.D. SCHWIETERS, J.J. KUSZEWSKI,N. TJANDRA, AND REMARK 3 G.M. CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 100 STRUCTUREWS WERE CALCULATED, THE MINIMIZED AVERAGE FROM THE 15 REMARK 3 LOWEST ENERGY STRUCTURES IS PRESENTED. CONSTRAINTS USED: 423 REMARK 3 DISTANCE, 63 TORSION ANGLE, 117 ORIENTATION (RDC). THE DELPIC REMARK 3 DATABASE WAS EMPLOYED IN THE REFINEMENT AS FOLLOWS: TORSION ANGLE REMARK 3 DATABASE ACTIVE FOR ALL RESIDUES, BASE-BASE POSITIONAL DATABASE REMARK 3 ACTIVE FOR RESIDUES 907-912, 914-916, AND 921-929. REMARK 3 DELPHIC DATABASE REFERENCE: CLORE, G.M. KUSZEWSKI, J. J. AM. CHEM. REMARK 3 SOC. 125: 1518-1525 REMARK 4 REMARK 4 1S2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021281. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 25 MM NACL, 10 MM NAPI REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : RNA RESIDUES 907-929 FROM NRS REMARK 210 (NRS23) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNN-COSY; DQF- REMARK 210 COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 4.1, VNMR 6.1C, NMRVIEW REMARK 210 5.0.4 REMARK 210 METHOD USED : SIMULATED ANNEALING. TORSION REMARK 210 ANGLE DYNAMICS IN REFINEMENT. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: EXCHANGEABLE PROTON SPECTRA COLLECTED AT 15 CELSIUS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' U A 917 H5' U A 918 1.48 REMARK 500 OP1 U A 920 H5' A A 921 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 G A 919 N7 G A 919 C8 -0.040 REMARK 500 G A 919 C8 G A 919 N9 -0.054 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 G A 907 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 907 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 908 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 908 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 909 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 909 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 910 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 910 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A A 911 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 912 C3' - C2' - C1' ANGL. DEV. = 6.4 DEGREES REMARK 500 G A 912 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 912 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 G A 914 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 914 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 915 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 915 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 U A 917 O4' - C4' - C3' ANGL. DEV. = 7.7 DEGREES REMARK 500 U A 917 C4' - C3' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 U A 917 C3' - C2' - C1' ANGL. DEV. = 9.9 DEGREES REMARK 500 U A 917 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 U A 918 C4' - C3' - O3' ANGL. DEV. = -14.0 DEGREES REMARK 500 U A 918 C2' - C3' - O3' ANGL. DEV. = 16.4 DEGREES REMARK 500 U A 918 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U A 918 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 G A 919 C4' - C3' - O3' ANGL. DEV. = 13.4 DEGREES REMARK 500 G A 919 C2' - C3' - O3' ANGL. DEV. = -16.5 DEGREES REMARK 500 G A 919 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 919 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 U A 920 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES REMARK 500 U A 920 C2' - C3' - O3' ANGL. DEV. = 9.9 DEGREES REMARK 500 U A 920 C3' - C2' - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 A A 921 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES 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 U A 917 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1S2F A 907 929 PDB 1S2F 1S2F 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