+Open data
-Basic information
Entry | Database: PDB / ID: 4w2p | ||||||
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Title | Anti-Marburgvirus Nucleoprotein Single Domain Antibody C | ||||||
Components | Anti-Marburgvirus Nucleoprotein Single Domain Antibody C | ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | ACETATE ION Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Taylor, A.B. / Garza, J.A. | ||||||
Citation | Journal: Front Immunol / Year: 2017 Title: Unveiling a Drift Resistant Cryptotope withinMarburgvirusNucleoprotein Recognized by Llama Single-Domain Antibodies. Authors: Garza, J.A. / Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w2p.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w2p.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 4w2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w2p_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 4w2p_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 4w2p_validation.xml.gz | 23 KB | Display | |
Data in CIF | 4w2p_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/4w2p ftp://data.pdbj.org/pub/pdb/validation_reports/w2/4w2p | HTTPS FTP |
-Related structure data
Related structure data | 4w2oC 4w2qC 6apoSC 6appC 6apqC 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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Unit cell |
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-Components
#1: Antibody | Mass: 14023.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) Description: Semi-synthetic single pot library Nomad 1 based upon Lama glama Plasmid: pecan73 / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-NA / | #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: 1.89 Å3/Da / Density % sol: 34.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% polyethylene glycol 550 monomethyl ether/polyethylene glycol 20000, 0.1M carboxylic acids mix (sodium formate, ammonium acetate, sodium citrate, sodium/potassium tartrate, sodium oxamate) ...Details: 30% polyethylene glycol 550 monomethyl ether/polyethylene glycol 20000, 0.1M carboxylic acids mix (sodium formate, ammonium acetate, sodium citrate, sodium/potassium tartrate, sodium oxamate), 0.1M imidazole/MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→48.65 Å / Num. obs: 36665 / % possible obs: 91.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.3 Å2 / Rpim(I) all: 0.058 / Rsym value: 0.063 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.77→1.86 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5165 / Rpim(I) all: 0.332 / Rsym value: 0.39 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6APO Resolution: 1.77→26.772 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→26.772 Å
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Refine LS restraints |
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LS refinement shell |
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