HEADER RNA 23-JUN-00 1F79 TITLE SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT TITLE 2 OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT(III) HEXAMMINE, NMR, TITLE 3 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P4 STEM; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED FROM DNA OLOGONUCLEOTIDE TEMPLATE BY T7 SOURCE 4 RNA POLYMERASE KEYWDS RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, C70U KEYWDS 2 MUTANT, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE KEYWDS 3 COMPLEX, RNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.SCHMITZ,I.TINOCO JR. REVDAT 3 16-FEB-22 1F79 1 REMARK REVDAT 2 24-FEB-09 1F79 1 VERSN REVDAT 1 09-OCT-00 1F79 0 JRNL AUTH M.SCHMITZ,I.TINOCO JR. JRNL TITL SOLUTION STRUCTURE AND METAL-ION BINDING OF THE P4 ELEMENT JRNL TITL 2 FROM BACTERIAL RNASE P RNA. JRNL REF RNA V. 6 1212 2000 JRNL REFN ISSN 1355-8382 JRNL PMID 10999599 JRNL DOI 10.1017/S1355838200000881 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, X-PLOR 3.841 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AVERAGE STRUCTURE IS BASED ON REMARK 3 SUPERPOSITION OF 12 CONVERGED STRUCTURES AFTER REFINEMENT. THE REMARK 3 AVERAGE RMS DEVIATION BETWEEN THE ENSEMBLE AND THE AVERAGE REMARK 3 STRUCTURE IS 1.5 ANGSTROM. A TOTAL OF 268 NOE-DERIVED REMARK 3 INTRAMOLECULAR DISTANCE CONSTRAINTS, 171 DIHEDRAL RESTRAINT AND REMARK 3 49 DISTANCE RESTRAINTS FROM HYDROGEN BONDS WERE USED IN THE REMARK 3 REFINEMENT. 12 NOE DERIVED INTERMOLECULAR DISTANCE CONSTRAINTS REMARK 3 WERE USED TO LOCALIZE THE BOUND COBALT (III) HEXAMMINE REMARK 4 REMARK 4 1F79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011330. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 288; 288; 288 REMARK 210 PH : 6.5; 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 100 MM NA; 100 MM NA; 100 MM NA, REMARK 210 10 MM MG; 100 MM NA, 3 MM CO(NH3) REMARK 210 6 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM P4M RNA; 100 MM SODIUM REMARK 210 CHLORIDE; 10 MM PHOSPHATE BUFFER; REMARK 210 90% H2O, 10% D2O; 2 MM P4M RNA; REMARK 210 100 MM SODIUM CHLORIDE; 10 MM REMARK 210 PHOSPHATE BUFFER; 99.96% D2O; 2 REMARK 210 MM P4M RNA; 100 MM SODIUM REMARK 210 CHLORIDE; 10 MM MAGNESIUM REMARK 210 CHLORIDE; 10 MM PHOSPHATE BUFFER; REMARK 210 90% H2O, 10% D2O; 2 MM P4M RNA; REMARK 210 100 MM SODIUM CHLORIDE; 3 MM REMARK 210 HEXAMMINE COBALT CHLORIDE; 10 MM REMARK 210 PHOSPHATE BUFFER; 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 31P-1H-COSY; REMARK 210 13C-1H-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95, X-PLOR 3.841 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 : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES AND 13C AND 31P HETERONUCLEAR TECHNIQUES REMARK 210 AT NATURAL ABUNDANCE. INTERMOLECULAR NOE CROSSPEAKS BETWEEN RNA REMARK 210 PROTONS AND COBALT (III) HEXAMMINE PROTONS AND DERIVED REMARK 210 INTERMOLECULAR DISTANCE CONSTRAINTS WERE USED TO DETERMINE THE REMARK 210 SITE OF COBALT (III) HEXAMMINE BINDING IN THE COMPLEX STRUCTURE 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 O6 G A 1 H41 C A 27 1.59 REMARK 500 REMARK 500 REMARK: NULL 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: 1F6Z RELATED DB: PDB REMARK 900 1F6Z SHOWS THE STRUCTURE OF THE FREE C70U MUTANT P4 STEM REMARK 900 OLIGORIBONUCLEOTIDE REMARK 900 RELATED ID: 1F6X RELATED DB: PDB REMARK 900 1F6X SHOWS THE STRUCTURE OF THE FREE WILDTYPE P4 STEM REMARK 900 OLIGORIBONUCLEOTIDE DBREF 1F79 A 1 27 PDB 1F79 1F79 1 27 SEQRES 1 A 27 G G A A G U U 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 5 G A 5 U A 6 C A 20 G A 21 SITE 2 AC1 5 C A 23 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