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Yorodumi- PDB-4a5u: Turnip yellow mosaic virus proteinase and Escherichia coli 30S ri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a5u | ||||||
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Title | Turnip yellow mosaic virus proteinase and Escherichia coli 30S ribosomal S15 | ||||||
Components |
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Keywords | TRANSFERASE/RNA BINDING PROTEIN / TRANSFERASE-RNA BINDING PROTEIN COMPLEX / CYSTEINE PROTEINASE | ||||||
Function / homology | Function and homology information mRNA methyltransferase activity / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / RNA-directed RNA polymerase ...mRNA methyltransferase activity / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | TURNIP YELLOW MOSAIC VIRUS ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å | ||||||
Authors | Robin, C. / Beaurepaire, L. / Bressanelli, S. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: A Compact Viral Processing Proteinase/Ubiquitin Hydrolase from the Otu Family. Authors: Lombardi, C. / Ayach, M. / Beaurepaire, L. / Chenon, M. / Andreani, J. / Guerois, R. / Jupin, I. / Bressanelli, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: In Praise of Impurity: 30S Ribosomal S15 Protein-Assisted Crystallization of Turnip Yellow Mosaic Virus Proteinase. Authors: Robin, C. / Beaurepaire, L. / Chenon, M. / Jupin, I. / Bressanelli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a5u.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a5u.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 4a5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a5u_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 4a5u_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 4a5u_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4a5u_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a5u ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a5u | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17778.873 Da / Num. of mol.: 1 Fragment: POLYPROTEIN PROCESSING PROTEINASE DOMAIN, RESIDUES 728-879 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TURNIP YELLOW MOSAIC VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10358, RNA-directed RNA polymerase |
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#2: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-89 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / References: UniProt: E8Y371 |
#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: 3.99 Å3/Da / Density % sol: 69 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES PH 7.5 2.5 M AMMONIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.5 Å / Num. obs: 29613 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 27.24 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2→39.029 Å / SU ML: 0.56 / σ(F): 2 / Phase error: 18.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.886 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.029 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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