1F78 - Header Asymmetric Unit

HEADER RNA 26-JUN-00 1F78

TITLE SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM TITLE 2 OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE, TITLE 3 NMR, MINIMIZED AVERAGE STRUCTURE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA RIBOZYME, P4 DOMAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P4 STEM; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ENZYMATICALLY SYNTHESIZED FROM DNA SOURCE 4 OLOGONUCLEOTIDE TEMPLATE BY T7 RNA POLYMERASE

KEYWDS RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, KEYWDS 2 METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE KEYWDS 3 COMPLEX

EXPDTA SOLUTION NMR

MDLTYP MINIMIZED AVERAGE

AUTHOR M.SCHMITZ,I.TINOCO JR.

REVDAT 2 24-FEB-09 1F78 1 VERSN REVDAT 1 09-OCT-00 1F78 0

JRNL AUTH M.SCHMITZ,I.TINOCO JR. JRNL TITL SOLUTION STRUCTURE AND METAL-ION BINDING OF THE P4 JRNL TITL 2 ELEMENT 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 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.84 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AVERAGE STRUCTURE IS BASED ON REMARK 3 SUPERPOSITION OF 11 CONVERGED STRUCTURES AFTER REFINEMENT. THE REMARK 3 AVERAGE RMS DEVIATION BETWEEN THE ENSEMBLE AND THE AVERAGE REMARK 3 STRUCTURE IS 1.7 ANGSTROM. A TOTAL OF 266 NOE-DERIVED REMARK 3 INTRAMOLECULAR DISTANCE CONSTRAINTS, 164 DIHEDRAL RESTRAINT REMARK 3 AND 48 DISTANCE RESTRAINTS FROM HYDROGEN BONDS WERE USED IN REMARK 3 THE REFINEMENT. 12 NOE DERIVED INTERMOLECULAR DISTANCE REMARK 3 CONSTRAINTS WERE USED TO LOCALIZE THE BOUND COBALT (III) REMARK 3 HEXAMMINE

REMARK 4 REMARK 4 1F78 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-00. REMARK 100 THE RCSB ID CODE IS RCSB011329.

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 REMARK 210 NA, 10 MM MG; 100 MM NA, 3 MM REMARK 210 CO(NH3)6 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM P4 RNA; 100 MM SODIUM REMARK 210 CHLORIDE; 10 MM PHOSPHATE REMARK 210 BUFFER; 90% H2O, 10% D2O; 2 MM REMARK 210 P4 RNA; 100 MM SODIUM REMARK 210 CHLORIDE; 10 MM PHOSPHATE REMARK 210 BUFFER; 99.96% D2O; 2 MM P4 REMARK 210 RNA; 100 MM SODIUM CHLORIDE; REMARK 210 10 MM MAGNESIUM CHLORIDE; 10 REMARK 210 MM PHOSPHATE BUFFER; 90% H2O, REMARK 210 10% D2O; 2 MM P4 RNA; 100 MM REMARK 210 SODIUM CHLORIDE; 3 MM REMARK 210 HEXAMMINE COBALT CHLORIDE; 10 REMARK 210 MM PHOSPHATE BUFFER; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, 31P-1H- REMARK 210 COSY, 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 : XWINNMR 3.1, FELIX 95, X-PLOR REMARK 210 3.84 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 REMARK 210 TECHNIQUES AT NATURAL ABUNDANCE. INTERMOLECULAR NOE CROSSPEAKS REMARK 210 BETWEEN RNA PROTONS AND COBALT (III) HEXAMMINE PROTONS AND REMARK 210 DERIVED INTERMOLECULAR DISTANCE CONSTRAINTS WERE USED TO REMARK 210 DETERMINE THE SITE OF COBALT (III) HEXAMMINE BINDING IN THE REMARK 210 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 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 1F6X SHOWS THE STRUCTURE OF THE FREE WILDTYPE P4 STEM REMARK 900 OLIGORIBONUCLEOTIDE REMARK 900 RELATED ID: 1F6Z RELATED DB: PDB REMARK 900 1F6Z SHOWS THE STRUCTURE OF THE FREE C70U MUTANT P4 STEM REMARK 900 OLIGORIBONUCLEOTIDE

DBREF 1F78 A 1 27 PDB 1F78 1F78 1 27

SEQRES 1 A 27 G G A A G U 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 5 C A 8 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