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Yorodumi- PDB-3vsm: The crystal structure of novel chondroition lyase ODV-E66, baculo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vsm | ||||||
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Title | The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein | ||||||
Components | Occlusion-derived virus envelope protein E66 | ||||||
Keywords | LYASE ACTIVATOR / alpha/alpha troid / beta-sandwich | ||||||
Function / homology | Function and homology information Lyases; Carbon-oxygen lyases; Acting on polysaccharides / host cell cytoplasm / lyase activity / viral envelope / host cell nucleus / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Autographa californica nucleopolyhedrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kawaguchi, Y. / Sugiura, N. / Kimata, K. / Kimura, M. / Kakuta, Y. | ||||||
Citation | Journal: To be Published Title: The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein Authors: Kawaguchi, Y. / Sugiura, N. / Kimata, K. / Kimura, M. / Kakuta, Y. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Crystallization and X-ray diffraction analysis of chondroitin lyase from baculovirus: envelope protein ODV-E66. Authors: Kawaguchi, Y. / Sugiura, N. / Onishi, M. / Kimata, K. / Kimura, M. / Kakuta, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vsm.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vsm.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vsm_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 3vsm_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 3vsm_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 3vsm_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/3vsm ftp://data.pdbj.org/pub/pdb/validation_reports/vs/3vsm | HTTPS FTP |
-Related structure data
-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: 74368.164 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 67-704 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Autographa californica nucleopolyhedrovirus Gene: P79 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00704 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE EXPERIMENT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50mM Tri-HCl pH8.0, 100mM NaCl, 0.02M citric acid, 0.08M Bis-Tris propane pH8.8, 18 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 68227 / Num. obs: 68227 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.094 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.138 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 28.829 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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