HEADER RNA 23-JAN-05 1YN1 TITLE SOLUTION STRUCTURE OF THE VS RIBOZYME STEM-LOOP V IN THE TITLE 2 PRESENCE OF MGCL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VS RIBOZYME STEM-LOOP V; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SL5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS DERIVED FROM THE SOURCE 4 NEUROSPORA VARKUD SATELLITE RIBOZYME KEYWDS U-TURN; HAIRPIN; MAGNESIUM IONS, RNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR D.O.CAMPBELL,P.LEGAULT REVDAT 3 24-FEB-09 1YN1 1 VERSN REVDAT 2 19-SEP-06 1YN1 1 REVDAT 1 24-JAN-06 1YN1 0 JRNL AUTH D.O.CAMPBELL,P.BOUCHARD,G.DESJARDINS,P.LEGAULT JRNL TITL NMR STRUCTURE OF VARKUD SATELLITE RIBOZYME JRNL TITL 2 STEM-LOOP V IN THE PRESENCE OF MAGNESIUM IONS AND JRNL TITL 3 LOCALIZATION OF METAL-BINDING SITES JRNL REF BIOCHEMISTRY V. 45 10591 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16939211 JRNL DOI 10.1021/BI0607150 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.O.CAMPBELL,P.LEGAULT REMARK 1 TITL NMR STRUCTURE OF THE VS RIBOZYME STEM-LOOP V RNA REMARK 1 TITL 2 AND MAGNESIUM-ION BINDING FROM CHEMICAL-SHIFT REMARK 1 TITL 3 MAPPING REMARK 1 REF TO BE PUBLISHED 2005 REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH-2.0.6 REMARK 3 AUTHORS : BRUNGER, A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CONFORMER 1 REPRESENTS THE MINIMIZED REMARK 3 AVERAGE STRUCTURE, THE 10 FOLLOWING STRUCTURES REPRESENT THE REMARK 3 ENSEMBLE OF LOW-ENERGY STRUCTURES REMARK 4 REMARK 4 1YN1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-05. REMARK 100 THE RCSB ID CODE IS RCSB031702. 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 : VARIABLE (SEE SAMPLE DETAILS) REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM TO 2.0 MM OF REMARK 210 UNLABELED, 15N, OR 13C/15N SL5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N CPMG-NOESY, 3D 13C- REMARK 210 EDITED HMQC-NOESY, 2D HNN- REMARK 210 COSY, 3D HCCH E.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 : X-PLOR NIH-2.0.6, NMRPIPE REMARK 210 MOST CURRENT, NMRVIEW 5.0.3, REMARK 210 MOLMOL 2K.2 REMARK 210 METHOD USED : SIMULATED ANNEALING; REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 69 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 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: NULL 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 690 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 705 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 705 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 690 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 705 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 705 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 690 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 705 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 705 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 690 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 143 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TBK RELATED DB: PDB REMARK 900 THE SAME RNA IN THE ABSENCE OF MAGNESIUM IONS REMARK 900 RELATED ID: 1YN2 RELATED DB: PDB REMARK 900 THE SAME RNA ALSO IN THE PRESENCE OF MAGNESIUM IONS BUT REMARK 900 WITH MODELED MANGANESE IONS DBREF 1YN1 A 690 706 PDB 1YN1 1YN1 690 706 SEQRES 1 A 17 G C G A G U U G A C U A C SEQRES 2 A 17 U C G 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 138 0 0 0 0 0 0 6 0 0 0 2 END