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Yorodumi- PDB-3h5x: Crystal Structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h5x | ||||||
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Title | Crystal Structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to Norovirus GII RNA polymerase | ||||||
Components |
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Keywords | Transferase/RNA / POLYMERASE-RNA COMPLEX / NON-NATURAL NUCLEOSIDE TRIPHOSPHATE ANALOG / CALICIVIRUS / Hydrolase / Nucleotide-binding / Nucleotidyltransferase / Protease / RNA replication / RNA-directed RNA polymerase / Thiol protease / Transferase / Transferase-RNA COMPLEX | ||||||
Function / homology | Function and homology information ribonucleoside triphosphate phosphatase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Norwalk virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å | ||||||
Authors | Zamyatkin, D.F. / Parra, F. / Machin, A. / Grochulski, P. / Ng, K.K.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site. Authors: Zamyatkin, D.F. / Parra, F. / Machin, A. / Grochulski, P. / Ng, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h5x.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h5x.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 3h5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h5x_validation.pdf.gz | 934.6 KB | Display | wwPDB validaton report |
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Full document | 3h5x_full_validation.pdf.gz | 941.4 KB | Display | |
Data in XML | 3h5x_validation.xml.gz | 25 KB | Display | |
Data in CIF | 3h5x_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/3h5x ftp://data.pdbj.org/pub/pdb/validation_reports/h5/3h5x | HTTPS FTP |
-Related structure data
Related structure data | 3h5yC 3bsoS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56843.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GST-fusion protein cleaved with thrombin / Source: (gene. exp.) Norwalk virus / Genus: Norovirus / Strain: AST6139/01/SP / Gene: polymerase / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q70ET3, RNA-directed RNA polymerase |
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-RNA chain , 2 types, 2 molecules PT
#2: RNA chain | Mass: 2557.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer RNA |
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#3: RNA chain | Mass: 2862.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template RNA |
-Non-polymers , 4 types, 450 molecules
#4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CSG / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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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: 2.71 Å3/Da / Density % sol: 54.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 160 g/L PEG 8000, 250 g/L Glycerol, 100 mM Tris-Cl, pH 7.0, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM mercaptoethanol, 1 g/L CHAPS, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2008 Details: WHITE BEAM SLITS, CRYO-COOLED FIRST AND SAGITTALLY BENT SECOND CRYSTAL OF DOUBLE CRYSTAL MONOCHROMATOR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→20 Å / Num. all: 65879 / Num. obs: 65879 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.94 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.77→1.97 Å / Rmerge(I) obs: 0.67 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3BSO Resolution: 1.77→19.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.751 / SU ML: 0.086 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Total num. of bins used: 20
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