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Yorodumi- PDB-1hi0: RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hi0 | ||||||
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Title | RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus initiation complex | ||||||
Components |
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Keywords | RNA POLYMERASE / VIRAL POLYMERASE | ||||||
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 | BACTERIOPHAGE PHI-6 (bacteriophage) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Grimes, J.M. / Butcher, S.J. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I. | ||||||
Citation | Journal: Nature / Year: 2001 Title: A Mechanism for Initiating RNA-Dependent RNA Polymerization Authors: Butcher, S.J. / Grimes, J.M. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary X-Ray Crystallographic Studies on the Bacteriophage Phi6 RNA-Dependent RNA Polymerase Authors: Butcher, S.J. / Makeyev, E.V. / Grimes, J.M. / Stuart, D.I. / Bamford, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hi0.cif.gz | 396.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hi0.ent.gz | 336.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/1hi0 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/1hi0 | HTTPS FTP |
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-Related 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:
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Details | THE PROTEIN IS ACTIVE AS A MONOMER |
-Components
#1: DNA chain | Mass: 1445.985 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: 5 NUCLEOTIDE DNA VERSION OF OPTIMUM RNA TEMPLATE #2: Protein | Mass: 74903.203 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE PHI-6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11124 #3: Chemical | #4: Chemical | ChemComp-GTP / #5: Chemical | ChemComp-MG / Compound details | P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID. IT IS RESPONSIBLE FOR GENOMIC ...P2 IS ONE OF THE 4 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: 2.95 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||
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Crystal grow | pH: 6.7 Details: 1:1 PROTEIN(5MG/ML)+TEMPLATE WELL SOLUTION: 10% PEG 8000, 0.1M MES, 2 MM MNCL2, pH 6.70 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting dropDetails: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, 56, 1473. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9724 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 56000 / % possible obs: 95 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.1 / % possible all: 86 |
Reflection shell | *PLUS % possible obs: 86 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY TBA Resolution: 3→20 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refine analyze | Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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