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Yorodumi- PDB-1f7i: SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM C70U MUTAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f7i | ||||||
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Title | SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE ,NMR, ENSEMBLE OF 12 STRUCTURES | ||||||
Components | RNASE P RNA RIBOZYME, P4 DOMAIN | ||||||
Keywords | RNA / RIBONUCLEASE P / RIBOZYME / TRANSFER RNA PROCESSING / P4 STEM / C70U MUTANT / METAL BINDING SITE / METAL COMPLEX / COBALT (III) HEXAMMINE COMPLEX | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / restrained molecular dynamics; simulated annealing | ||||||
Authors | Schmitz, M. / Tinoco Jr., I. | ||||||
Citation | Journal: RNA / Year: 2000 Title: Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA. Authors: Schmitz, M. / Tinoco Jr., I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f7i.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f7i.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f7i_validation.pdf.gz | 331.8 KB | Display | wwPDB validaton report |
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Full document | 1f7i_full_validation.pdf.gz | 407 KB | Display | |
Data in XML | 1f7i_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1f7i_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/1f7i ftp://data.pdbj.org/pub/pdb/validation_reports/f7/1f7i | HTTPS FTP |
-Related structure data
Related structure data | 1f6xC 1f6zC 1f78C 1f79C 1f7fC 1f7gC 1f7hC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 8634.127 Da / Num. of mol.: 1 / Fragment: P4 STEM / Mutation: C70U / Source method: obtained synthetically Details: synthesized from DNA oligonucleotide template by T7 RNA polymerase |
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#2: Chemical | ChemComp-NCO / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Distance constraints derived from intermolecular NOE ...Text: This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Distance constraints derived from intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons were used to determine the site of cobalt (III) hexammine binding in the complex structure |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained molecular dynamics; simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 268 NOE derived distance constraints, 171 dihedral restraints and 49 distance restraints from hydrogen bonds. 12 NOE derived intermolecular distance ...Details: The structures are based on a total of 268 NOE derived distance constraints, 171 dihedral restraints and 49 distance restraints from hydrogen bonds. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt(III) hexammine. The 12 structures with lowest NOE and dihedral angle violation energies are presented | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 12 |