[English] 日本語
Yorodumi- PDB-3bsn: Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bsn | ||||||
---|---|---|---|---|---|---|---|
Title | Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA | ||||||
Components |
| ||||||
Keywords | Transferase/RNA / RNA-dependent RNA polymerase / viral replication / antiviral enzyme inhibitor / Helicase / Hydrolase / Nucleotide-binding / Nucleotidyltransferase / RNA replication / RNA-directed RNA polymerase / Transferase / Transferase-RNA COMPLEX | ||||||
Function / homology | Function and homology information ribonucleoside triphosphate phosphatase activity / viral RNA genome replication / cysteine-type endopeptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zamyatkin, D.F. / Ng, K.K.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase. Authors: Zamyatkin, D.F. / Parra, F. / Alonso, J.M. / Harki, D.A. / Peterson, B.R. / Grochulski, P. / Ng, K.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bsn.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bsn.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/3bsn ftp://data.pdbj.org/pub/pdb/validation_reports/bs/3bsn | HTTPS FTP |
---|
-Related structure data
Related structure data | 3bsoC 1sh0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 Source: (gene. exp.) Norwalk virus / Genus: Norovirus / Strain: Ast6139/01/Sp / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q70ET3, RNA-directed RNA polymerase |
---|
-RNA chain , 2 types, 2 molecules PT
#2: RNA chain | Mass: 2557.577 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: chemically synthesized self-complementary RNA oligonucleotide with 2-base overhang |
---|---|
#3: RNA chain | Mass: 2907.756 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: chemically synthesized self-complementary RNA oligonucleotide that was extended by a single 5-nitrocytidine monophosphate residue during crystallization |
-Non-polymers , 4 types, 355 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-N5C / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% (w/v) PEG 8000, 25% (w/v) glycerol, 100 mM Tris-HCl, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM 2-mercaptoethanol, 0.1% (w/v) CHAPS, 0.5 mM RNA duplex, 1 mM NTP, 0.03 mM polymerase, pH 7. ...Details: 16% (w/v) PEG 8000, 25% (w/v) glycerol, 100 mM Tris-HCl, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM 2-mercaptoethanol, 0.1% (w/v) CHAPS, 0.5 mM RNA duplex, 1 mM NTP, 0.03 mM polymerase, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2007 Details: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM) |
Radiation | Monochromator: sagittally bent second crystal of 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: 1.8→30 Å / Num. all: 58959 / Num. obs: 58959 / % possible obs: 93.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.3 / Num. unique all: 11566 / Rsym value: 0.614 / % possible all: 78.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1SH0 Resolution: 1.8→19.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.291 / SU ML: 0.1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 32.254 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
|