Header list of 1f78.pdb file
Complete list - 16 202 Bytes
HEADER RNA 26-JUN-00 1F78
TITLE SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE
TITLE 2 COMPLEXED WITH COBALT (III) HEXAMINE, NMR, MINIMIZED AVERAGE
TITLE 3 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 OLOGONUCLEOTIDE
SOURCE 4 TEMPLATE BY T7 RNA POLYMERASE
KEYWDS RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, METAL
KEYWDS 2 BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE COMPLEX, RNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.SCHMITZ,I.TINOCO JR.
REVDAT 3 16-FEB-22 1F78 1 REMARK
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 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 3.84
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 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 AND
REMARK 3 48 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 1F78 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_1000011329.
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 P4 RNA; 100 MM SODIUM
REMARK 210 CHLORIDE; 10 MM PHOSPHATE BUFFER;
REMARK 210 90% H2O, 10% D2O; 2 MM P4 RNA;
REMARK 210 100 MM SODIUM CHLORIDE; 10 MM
REMARK 210 PHOSPHATE BUFFER; 99.96% D2O; 2
REMARK 210 MM P4 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 P4 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 3.84
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 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 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
Complete list - 16 202 Bytes