+Open data
-Basic information
Entry | Database: PDB / ID: 5ush | ||||||
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Title | Structure of vaccinia virus D8 protein bound to human Fab vv66 | ||||||
Components |
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Keywords | VIRAL PROTEIN/Immune system / viral protein / antibody / Fab / Immune response / Ig fold / VIRAL PROTEIN-Immune system complex | ||||||
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 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Zajonc, D.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8. Authors: Matho, M.H. / Schlossman, A. / Gilchuk, I.M. / Miller, G. / Mikulski, Z. / Hupfer, M. / Wang, J. / Bitra, A. / Meng, X. / Xiang, Y. / Kaever, T. / Doukov, T. / Ley, K. / Crotty, S. / Peters, ...Authors: Matho, M.H. / Schlossman, A. / Gilchuk, I.M. / Miller, G. / Mikulski, Z. / Hupfer, M. / Wang, J. / Bitra, A. / Meng, X. / Xiang, Y. / Kaever, T. / Doukov, T. / Ley, K. / Crotty, S. / Peters, B. / Hsieh-Wilson, L.C. / Crowe, J.E. / 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 | 5ush.cif.gz | 511.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ush.ent.gz | 422.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ush.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ush_validation.pdf.gz | 468.3 KB | Display | wwPDB validaton report |
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Full document | 5ush_full_validation.pdf.gz | 476 KB | Display | |
Data in XML | 5ush_validation.xml.gz | 44 KB | Display | |
Data in CIF | 5ush_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/5ush ftp://data.pdbj.org/pub/pdb/validation_reports/us/5ush | HTTPS FTP |
-Related structure data
Related structure data | 5uslC 6b9jC 4e9oS 4fqqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27965.414 Da / Num. of mol.: 2 / Fragment: UNP residues 1-235 Source method: isolated from a genetically manipulated source Details: CAH domain / Source: (gene. exp.) Vaccinia virus / Gene: VAC_DPP17_124, VACAC2_124, VACCL3_124 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1M1K6 #2: Antibody | Mass: 24071.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Antibody | Mass: 22331.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 200 mM sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→38.76 Å / Num. obs: 75859 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.23→2.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 10614 / Rpim(I) all: 0.405 / % possible all: 97.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E9O, 4FQQ Resolution: 2.3→38.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 20.504 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.236 / 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: 52.615 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→38.51 Å
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