HEADER RNA 18-AUG-98 2LDZ TITLE SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, TITLE 2 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEAD-DEPENDENT RIBOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LEADZYME; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: MOLECULE IS RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PREPARED BY IN VITRO TRANSCRIPTION FROM SOURCE 4 SYNTHETIC DNA TEMPLATE KEYWDS CATALYTIC RNA, INTERNAL LOOPS, LEADZYME, NMR SPECTROSCOPY, KEYWDS 2 RNA STRUCTURE EXPDTA SOLUTION NMR AUTHOR C.G.HOOGSTRATEN,P.LEGAULT,A.PARDI REVDAT 2 24-FEB-09 2LDZ 1 VERSN REVDAT 1 23-FEB-99 2LDZ 0 JRNL AUTH C.G.HOOGSTRATEN,P.LEGAULT,A.PARDI JRNL TITL NMR SOLUTION STRUCTURE OF THE LEAD-DEPENDENT JRNL TITL 2 RIBOZYME: EVIDENCE FOR DYNAMICS IN RNA CATALYSIS. JRNL REF J.MOL.BIOL. V. 284 337 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9813122 JRNL DOI 10.1006/JMBI.1998.2182 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.LEGAULT,C.G.HOOGSTRATEN,E.METLITZKY,A.PARDI REMARK 1 TITL ORDER, DYNAMICS AND METAL-BINDING IN THE REMARK 1 TITL 2 LEAD-DEPENDENT RIBOZYME REMARK 1 REF J.MOL.BIOL. V. 284 325 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.PAN,B.DICHTL,O.C.UHLENBECK REMARK 1 TITL PROPERTIES OF AN IN VITRO SELECTED PB2+ CLEAVAGE REMARK 1 TITL 2 MOTIF REMARK 1 REF BIOCHEMISTRY V. 33 9561 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.PAN,O.C.UHLENBECK REMARK 1 TITL A SMALL METALLORIBOZYME WITH A TWO-STEP MECHANISM REMARK 1 REF NATURE V. 358 560 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH T.PAN,O.C.UHLENBECK REMARK 1 TITL IN VITRO SELECTION OF RNAS THAT UNDERGO AUTOLYTIC REMARK 1 TITL 2 CLEAVAGE WITH PB2+ REMARK 1 REF BIOCHEMISTRY V. 31 3887 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A COMPLETE SET OF REFINEMENT MACROS, REMARK 3 ALONG WITH ASSOCIATED FILES, IS AVAILABLE UPON REQUEST TO THE REMARK 3 AUTHORS. REMARK 4 REMARK 4 2LDZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0.1 M REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : H2O/D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, CPMG-NOESY, BD-NOESY, REMARK 210 CBD-NOESY, NOESY-HSQC, CBD- REMARK 210 NOESY-HSQC, HMQC-NOESY-HSQC, REMARK 210 HCCH-E.COSY, DIRECTED HCC- REMARK 210 TOCSY-CCH-E.COSY, SPIN-ECHO REMARK 210 DIFFERENCE CT-HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS, UNITYINOVA, DMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING FROM REMARK 210 RANDOM TORSION ANGLES REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE VIOLATIONS GREATER REMARK 210 THAN 0.3 A, NO DIHEDRAL REMARK 210 VIOLATIONS GREATER THAN 3 REMARK 210 DEGREES, GOOD STEREOCHEMICAL REMARK 210 QUALITY, TOTAL ENERGY LESS REMARK 210 THAN -120 KCAL/MOL, NOE REMARK 210 PSEUDOENERGY LESS THAN 4 KCAL/ REMARK 210 MOL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED FROM DISTANCE AND TORSION REMARK 210 ANGLE RESTRAINTS DERIVED USING UNLABELED, 15N-LABELED, AND REMARK 210 13C, 15N-LABELED SAMPLES OF THE LEADZYME PREPARED BY IN VITRO REMARK 210 TRANSCRIPTION. 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 19 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 22 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 24 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 24 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 29 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 29 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LDZ RELATED DB: PDB REMARK 900 ENSEMBLE OF 25 STRUCTURES DBREF 2LDZ A 1 30 PDB 2LDZ 2LDZ 1 30 SEQRES 1 A 30 G C G A C C G A G C C A G SEQRES 2 A 30 C G A A A G U U G G G A G SEQRES 3 A 30 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 MASTER 138 0 0 0 0 0 0 6 0 0 0 3 END