HEADER RNA 20-OCT-04 1XST TITLE SOLUTION STRUCTURE OF E.COLI RNASE P RNA P4 STEM, U69A MUTATION, TITLE 2 COMPLEXED WITH COBALT (III) HEXAMMINE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE P RNA P4 STEM; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ENZYMATICALLY SYNTHESIZED FROM DNA OLIGONUCLEOTIDE SOURCE 4 TEMPLATE NY T7 RNA POLYMERASE KEYWDS RIBONUCLEASE P RNA, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, U69A KEYWDS 2 MUTANT, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE KEYWDS 3 COMPLEX, RNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.SCHMITZ REVDAT 3 02-MAR-22 1XST 1 REMARK REVDAT 2 24-FEB-09 1XST 1 VERSN REVDAT 1 28-DEC-04 1XST 0 JRNL AUTH M.SCHMITZ JRNL TITL CHANGE OF RNASE P RNA FUNCTION BY SINGLE BASE MUTATION JRNL TITL 2 CORRELATES WITH PERTURBATION OF METAL ION BINDING IN P4 AS JRNL TITL 3 DETERMINED BY NMR SPECTROSCOPY JRNL REF NUCLEIC ACIDS RES. V. 32 6358 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15576680 JRNL DOI 10.1093/NAR/GKH961 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.2, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), A. BRUENGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AVERAGE STRUCTURE IS BASED ON THE REMARK 3 SUPERPOSITION OF 14 STRUCTURES AFTER REFINEMENT. THE AVERAGE RMS REMARK 3 DEVIATION BETWEEN THE ENSEMBLE AND THE AVERAGE STRUCTURE IS 1.85 REMARK 3 ANGSTROM. A TOTAL OF 290 NOE-DERIVED DISTANCE CONSTRAINTS, 245 REMARK 3 DIHEDRAL CONSTRAINTS AND 48 DISTANCE CONSTRAINTS FROM HYDROGEN REMARK 3 BONDS WERE USED IN REFINEMENT. 15 NOE DERIVED INTERMOLECULAR REMARK 3 DISTANCE CONSTRAINTS WERE USED TO LOCALIZE THE BOUND COBALT (III) REMARK 3 HEXAMMINE. REMARK 4 REMARK 4 1XST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030726. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 288 REMARK 210 PH : 6.4; 6.4 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL, 6 MM REMARK 210 CO(NH3)6CL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM P4 U69A RNA; 100MM NACL; REMARK 210 10MM PHOSPHATE BUFFER; 90% H2O, REMARK 210 10% D2O; 2MM P4 U69A RNA; 100MM REMARK 210 NACL; 10MM PHOSPHATE BUFFER; 100% REMARK 210 D2O; 2MM P4 U69A RNA; 100MM REMARK 210 NACL; 6MM HEXAMMINE COBALT REMARK 210 CHLORIDE; 10MM PHOSPHATE BUFFER; REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 31P-1H REMARK 210 -HETERO-COSY; 31P-1H-HETERO- REMARK 210 TOCSY-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, X-PLOR 3.1 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 AND SIMULATED ANNEALING 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: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR REMARK 210 TECHNIQUES AS WELL AS 13C AND 31P HETERONUCLEAR EXPERIMENTS REMARK 210 PERFORMED AT NATURAL ABUNDANCE. INTERMOLECULAR NOE CROSSPEAKS REMARK 210 BETWEEN RNA PROTONS AND COBALT (III) HEXAMMINE PROTONS AND REMARK 210 INTERMOLECULAR DISTANCE CONSTRAINTS DERIVED THEREOF WERE USED TO REMARK 210 DETERMINE THE SITE OF COBALT (III) HEXAMMINE BINDING. 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 28 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F6X RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF WILDTYPE RNASE P RNA P4 OLIGORIBONUCLEOTIDE REMARK 900 RELATED ID: 1F78 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF WILDTYPE RNASE P RNA P4 OLIGORIBONUCLEOTIDE, REMARK 900 COMPLEXED WITH COBALT (III) HEXAMMINE REMARK 900 RELATED ID: 1XSU RELATED DB: PDB REMARK 900 U69C/C70U MUTATIONS DBREF 1XST A 1 27 PDB 1XST 1XST 1 27 SEQRES 1 A 27 G G A A G A C C G G U C U SEQRES 2 A 27 U C G G A C C G G C U U C SEQRES 3 A 27 C HET NCO A 28 25 HETNAM NCO COBALT HEXAMMINE(III) FORMUL 2 NCO CO H18 N6 3+ SITE 1 AC1 3 G A 9 C A 20 G A 21 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