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Yorodumi- PDB-5ezq: Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ezq | ||||||
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Title | Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural protein 2 (nsP2) Cysteine Protease | ||||||
Components | Non-structural Protein 2 Cysteine Protease | ||||||
Keywords | HYDROLASE / VEEV / nsP2 / Cysteine protease / alphavirus | ||||||
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 / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / 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 / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / 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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Compton, J.R. / Legler, P.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease. Authors: Hu, X. / Compton, J.R. / Leary, D.H. / Olson, M.A. / Lee, M.S. / Cheung, J. / Ye, W. / Ferrer, M. / Southall, N. / Jadhav, A. / Morazzani, E.M. / Glass, P.J. / Marugan, J. / Legler, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ezq.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ezq.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ezq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ezq_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
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Full document | 5ezq_full_validation.pdf.gz | 431.3 KB | Display | |
Data in XML | 5ezq_validation.xml.gz | 15 KB | Display | |
Data in CIF | 5ezq_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/5ezq ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ezq | HTTPS FTP |
-Related structure data
Related structure data | 5ezsC 2hwkS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 38341.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cys-477 is partially oxidized. Source: (gene. exp.) Venezuelan equine encephalitis virus (strain Trinidad donkey) Strain: Trinidad donkey / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS References: UniProt: P27282, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.44 % / Description: rod-shaped |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: JCSG+ Condition #15 (0.1 M Bicine pH 8.5, 20% PEG 6000) |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jan 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→63.72 Å / Num. obs: 40129 / % possible obs: 99.6 % / Redundancy: 6.01 % / Rsym value: 0.0406 / Net I/σ(I): 21.91 |
Reflection shell | Resolution: 1.66→1.76 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.3751 / Mean I/σ(I) obs: 3.24 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2hwk Resolution: 1.66→51.21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→51.21 Å
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