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Yorodumi- PDB-2hwk: Crystal Structure of Venezuelan Equine Encephalitis Alphavirus ns... -
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-Basic information
Entry | Database: PDB / ID: 2hwk | ||||||
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Title | Crystal Structure of Venezuelan Equine Encephalitis Alphavirus nsP2 Protease Domain | ||||||
Components | helicase nsP2 | ||||||
Keywords | HYDROLASE / Rossmann fold / alpha/beta/alpha / multi-domain | ||||||
Function / homology | Function and homology information O-acetyl-ADP-ribose deacetylase activity / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...O-acetyl-ADP-ribose deacetylase activity / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / RNA processing / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Venezuelan equine encephalitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.45 Å | ||||||
Authors | Russo, A.T. / White, M.A. / Watowich, S.J. | ||||||
Citation | Journal: Structure / Year: 2006 Title: The Crystal Structure of the Venezuelan Equine Encephalitis Alphavirus nsP2 Protease. Authors: Russo, A.T. / White, M.A. / Watowich, S.J. #1: Journal: To be Published Title: Structural Basis of Substrate Specificity in Venezuelan Equine Encephalitis nsP2 Protease Authors: Russo, A.T. / White, M.A. / Malmstrom, R. / Watowich, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hwk.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hwk.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hwk_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 2hwk_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 2hwk_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2hwk_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hwk ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hwk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36239.410 Da / Num. of mol.: 1 / Fragment: nsP2pro Source method: isolated from a genetically manipulated source Source: (gene. exp.) Venezuelan equine encephalitis virus (strain TC-83) Genus: Alphavirus / Species: Venezuelan equine encephalitis virus / Strain: TC-83 / Gene: NS / Plasmid: pETBlue1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLacI References: UniProt: P27282, UniProt: Q9WIJ1*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.0 M Ammonium Formate, 2% 2-Methyl-2, 4-pentanediol, 1% glycerol, 200 uM Zinc Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.3808 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2005 Details: Vertical collimating mirror, Toroidal focusing mirror, monochromator |
Radiation | Monochromator: Si(111) Channel Cut Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3808 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→43.37 Å / Num. all: 14092 / Num. obs: 14092 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.45→2.49 Å / Num. unique all: 653 / Rsym value: 0.286 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: None Resolution: 2.45→43.37 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1698628.21 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: PMB was used in the refinement. http://xray.utmb.edu/PMB.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.5126 Å2 / ksol: 0.376216 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→43.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.49 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 20
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Xplor file |
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