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Yorodumi- PDB-5vz1: Crystal structure of the Apo Antibody fragment (Fab) raised again... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vz1 | ||||||
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Title | Crystal structure of the Apo Antibody fragment (Fab) raised against C-terminal domain of Ebola nucleoprotein (EBOV, TAFV, BDBV strains) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ebola virus / Nucleoprotein / Fab / Antibody fragment | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.112 Å | ||||||
Authors | Radwanska, M.J. / Derewenda, U. / Kossiakoff, A. / Derewenda, Z.S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the Apo Antibody fragment (Fab) raised against C-terminal domain of Ebola nucleoprotein (EBOV, TAFV, BDBV strains) Authors: Radwanska, M.J. / Derewenda, U. / Kossiakoff, A. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vz1.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vz1.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 5vz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/5vz1 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/5vz1 | HTTPS FTP |
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-Related structure data
Related structure data | 6b6zC 5vkdS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 23396.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 25235.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | #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: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 90 mM imidazole, pH 8.0, 180 mM Zinc Acetate, 27% PEG 3000, 10 mM Chromium (III) chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→47.4 Å / Num. obs: 50593 / % possible obs: 93.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 27.8 Å2 / Net I/σ(I): 4.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VKD Resolution: 2.112→37.31 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.112→37.31 Å
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Refine LS restraints |
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LS refinement shell |
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