+Open data
-Basic information
Entry | Database: PDB / ID: 4e9o | ||||||
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Title | Vaccinia D8L ectodomain structure | ||||||
Components | IMV membrane protein | ||||||
Keywords | VIRAL PROTEIN / CAH alpha fold / Vp7 motif / beta sheet / cell surface chondroitin binding / viral entry / chondroitin sulfate | ||||||
Function / homology | Function and homology information regulation of pH / carbonate dehydratase activity / carbon dioxide transport / virion membrane / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Matho, M.H. / Zajonc, D.M. | ||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition by the Antibody LA5. Authors: Matho, M.H. / Maybeno, M. / Benhnia, M.R. / Becker, D. / Meng, X. / Xiang, Y. / Crotty, S. / Peters, B. / Zajonc, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e9o.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e9o.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e9o_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 4e9o_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 4e9o_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4e9o_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/4e9o ftp://data.pdbj.org/pub/pdb/validation_reports/e9/4e9o | HTTPS FTP |
-Related structure data
Related structure data | 4ebqC 4etqSC S: Starting model for refinement C: citing same article (ref.) |
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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: 31321.184 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 1-261) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Strain: Acambis clone 2000 / Gene: VACAC2_124, VACCL3_124, VAC_DPP17_124 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus BL21 / References: UniProt: Q1M1K6 | ||
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#2: Chemical | ChemComp-IOD / #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: 1.8 Å3/Da / Density % sol: 31.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 0.2 M sodium iodide, 20% PEG3350, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.100002 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2011 / Details: mirrors |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.100002 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→25.9 Å / Num. all: 40635 / Num. obs: 40635 / % possible obs: 99.3675 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.42→1.45 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2880 / Rsym value: 0.63 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ETQ Resolution: 1.42→25.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.241 / SU ML: 0.044 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 19.471 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→25.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 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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