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Yorodumi- PDB-3p06: Crystal structure of Tellina virus 1 VP4 protease in the form of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p06 | ||||||
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Title | Crystal structure of Tellina virus 1 VP4 protease in the form of an intra-molecular(cis)acyl-enzyme complex. | ||||||
Components | VP4 protein | ||||||
Keywords | HYDROLASE / cis-cleavage / intramolecular acyl-enzyme / ester-linkage / alpha/beta protein / protease / polyprotein processing / acyl-enzyme | ||||||
Function / homology | Function and homology information serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Tellina virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Chung, I.Y.W. / Paetzel, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal Structure of a Viral Protease Intramolecular Acyl-enzyme Complex: INSIGHTS INTO cis-CLEAVAGE AT THE VP4/VP3 JUNCTION OF TELLINA BIRNAVIRUS. Authors: Chung, I.Y. / Paetzel, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Expression, purification and crystallization of VP4 protease from Tellina virus 1. Authors: Chung, I.Y. / Paetzel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p06.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p06.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 3p06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/3p06 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p06 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20563.883 Da / Num. of mol.: 1 / Fragment: UNP residues 637-830 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tellina virus 1 / Gene: viral protein 4 (VP4) / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q2PBR5, EC: 3.4.21.115 |
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-Non-polymers , 6 types, 54 molecules
#2: Chemical | ChemComp-SO4 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-BME / | #5: Chemical | ChemComp-URE / | #6: Chemical | ChemComp-CL / | #7: 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: 2.55 Å3/Da / Density % sol: 51.86 % |
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Crystal grow | Temperature: 296 K / pH: 5 Details: reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 ...Details: reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 microliter of 0.2M urea as additive. To aid in crystal nucleation, this drop was seeded with 1 microliter of selenomethionine- labelled crystal from an older drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97893 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 28, 2010 Details: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR. |
Radiation | Monochromator: A DOUBLE CRYSTAL MONOCHROMATOR (DCM) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52 Å / Num. obs: 13466 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.3 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.221 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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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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