HEADER RNA 28-MAR-03 1OW9 TITLE NMR STRUCTURE OF THE ACTIVE CONFORMATION OF THE VS RIBOZYME TITLE 2 CLEAVAGE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: A MIMIC OF THE VS RIBOZYME HAIRPIN SUBSTRATE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VS RNA SUBSTRATE HAIRPIN; COMPND 5 SYNONYM: SL1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS DERIVED FROM THE SOURCE 4 NEUROSPORA VS RIBOZYME SUBSTRATE KEYWDS VS RIBOZYME, SUBSTRATE HAIRPIN, CLEAVAGE SITE, SHEARED G-A KEYWDS 2 BASE PAIRS, SHARED SHEARED G-A BASE PAIRS, MAGNESIUM ION KEYWDS 3 BINDING, GNRA TETRALOOP, RIBOZE ZIPPER, RNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR B.HOFFMANN,G.T.MITCHELL,P.GENDRON,F.MAJOR,A.A.ANDERSEN, AUTHOR 2 R.A.COLLINS,P.LEGAULT REVDAT 3 24-FEB-09 1OW9 1 VERSN REVDAT 2 17-JUN-03 1OW9 1 JRNL REVDAT 1 20-MAY-03 1OW9 0 JRNL AUTH B.HOFFMANN,G.T.MITCHELL,P.GENDRON,F.MAJOR, JRNL AUTH 2 A.A.ANDERSEN,R.A.COLLINS,P.LEGAULT JRNL TITL NMR STRUCTURE OF THE ACTIVE CONFORMATION OF THE JRNL TITL 2 VARKUD SATELLITE RIBOZYME CLEAVAGE SITE JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 7003 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12782785 JRNL DOI 10.1073/PNAS.0832440100 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.840 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FIRST MODEL IS THE MINIMIZED REMARK 3 AVERAGE STRUCTURE, THE LAST 10 REPRESENT THE ENSEMBLE OF REMARK 3 STRUCTURES REMARK 4 REMARK 4 1OW9 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 RCSB018730. 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 : 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM RNA U-13C,15N; 10 MM REMARK 210 D11-TRIS PH 7.0; 50 MM NACL; REMARK 210 0.2 MM EDTA; 0.05 MM NAN3; 1.1 REMARK 210 MM RNA U-13C,15N; 10 MM D11- REMARK 210 TRIS PH 7.0; 50 MM NACL; 0.2 REMARK 210 MM EDTA; 0.05 MM NAN3; 1.7 MM REMARK 210 RNA U-15N; 10 MM D11-TRIS PH REMARK 210 7.0; 50 MM NACL; 0.2 MM EDTA; REMARK 210 0.05 MM NAN3; 5.3 MM RNA U- REMARK 210 15N; 10 MM D11-TRIS PH 7.0; 50 REMARK 210 MM NACL; 0.2 MM EDTA; 0.05MM REMARK 210 NAN3; 1.7 MM RNA; 10 MM D11- REMARK 210 TRIS PH 7.0; 50 MM NACL; 0.2 REMARK 210 MM EDTA; 0.05 MM NAN3; 1.7 MM REMARK 210 RNA; 10 MM D11-TRIS PH 7.0; 50 REMARK 210 MM NACL; 0.2 MM EDTA; 0.05 MM REMARK 210 NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 13C/15N-EDITED HSQC-NOESY, REMARK 210 3D 13C-EDITED HMQC-NOESY, 2D REMARK 210 1H/15N CPMG-NOESY, 2D HNN- REMARK 210 COSY, 2D H(CN)N(H), 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.03, X- REMARK 210 PLOR 3.840, MOLMOL 2K.1 REMARK 210 METHOD USED : RESTRAINED MOLECULAR REMARK 210 DYNAMICS; SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 264 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E4P RELATED DB: PDB REMARK 900 STRUCTURE OF THE RIBOZYME SUBSTRATE HAIRPIN OF NEUROSPORA REMARK 900 VS RNA. A CLOSE LOOK AT THE CLEAVAGE SITE REMARK 900 RELATED ID: 1HWQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE VS RIBOZYME SUBSTRATE STEM-LOOP DBREF 1OW9 A 1 23 PDB 1OW9 1OW9 1 23 SEQRES 1 A 23 G A G C G A A G A C G A A SEQRES 2 A 23 A G U C G A G C U 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 MASTER 147 0 0 0 0 0 0 6 0 0 0 2 END