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Yorodumi- PDB-1uvn: The structural basis for RNA specificity and Ca2 inhibition of an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uvn | ||||||
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Title | The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 ca2+ inhibition complex | ||||||
Components |
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Keywords | POLYMERASE / RNA-DEPENDENT RNA POLYMERASE CA INHIBITION COMPLEX WITH 6NT RNA OLIGONUCLEOTIDE / GTP / MN / TRANSCRIPTION | ||||||
Function / homology | Function and homology information RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas phage phi6 (bacteriophage) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Salgado, P.S. / Makeyev, E.V. / Butcher, S. / Bamford, D. / Stuart, D.I. / Grimes, J.M. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase. Authors: Salgado, P.S. / Makeyev, E.V. / Butcher, S.J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uvn.cif.gz | 411 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uvn.ent.gz | 333.8 KB | Display | PDB format |
PDBx/mmJSON format | 1uvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uvn ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uvn | HTTPS FTP |
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-Related structure data
Related structure data | 1uviC 1uvjC 1uvkC 1uvlC 1uvmC 1hhsS S: Starting model for refinement 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1),Details | THE POLYMERASE IS A MONOMER IN SOLUTION, BUT SINCEIT IS IN COMPLEX WITH RNA IN THIS ENTRY, THE OLIGOMERIS ANNOTATED AS A DIMER | |
-Components
-Protein / RNA chain , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 74903.203 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phi6 (bacteriophage) / Gene: P2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase #2: RNA chain | Mass: 1790.069 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: COMMERCIALLY SUPPLIED BY OSWELL LTD / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 168 molecules
#3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-CA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | P2 IS ONE OF THE STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, RESPONSIBLE FOR GENOMIC ...P2 IS ONE OF THE STRUCTURAL |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.86 % / Description: DATA COLLECTED AT MN K EDGE | ||||||||||||||||||||||||
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Crystal grow | pH: 7.3 Details: 100MM HEPES PH7.3, 13% PEG 20000,2MM MNCL2, 2% EG, 0.036MG PROTEIN INCUBATED WITH 0.006MM 6NT RNA. SOAKING: 25MM CACL2 AND 40-60MM GTP (LITHIUM SALT), pH 7.30 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 6.7 / Method: vapor diffusion, sitting dropDetails: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, D56, 1473. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.894 |
Detector | Date: Apr 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.894 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 51586 / % possible obs: 96.9 % / Observed criterion σ(I): 1.5 / Redundancy: 17 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.6 / % possible all: 78.4 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. measured all: 880290 / Rmerge(I) obs: 0.151 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 78.4 % / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHS Resolution: 3→19.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1522098.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.331938 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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