+Open data
-Basic information
Entry | Database: PDB / ID: 6dwc | ||||||
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Title | Structure of the apo 4497 antibody Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Fab / wall teichoic acid / WTA / Staphylococcus aureus | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Fong, R. / Lupardus, P.J. | ||||||
Citation | Journal: MAbs / Year: 2018 Title: Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid. Authors: Fong, R. / Kajihara, K. / Chen, M. / Hotzel, I. / Mariathasan, S. / Hazenbos, W.L.W. / Lupardus, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dwc.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dwc.ent.gz | 151.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dwc_validation.pdf.gz | 467.8 KB | Display | wwPDB validaton report |
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Full document | 6dwc_full_validation.pdf.gz | 470.2 KB | Display | |
Data in XML | 6dwc_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 6dwc_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/6dwc ftp://data.pdbj.org/pub/pdb/validation_reports/dw/6dwc | HTTPS FTP |
-Related structure data
Related structure data | 6dw2C 6dwaC 6dwiC 4kvnS 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: Antibody | Mass: 26485.666 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: 25755.895 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: Chemical | ChemComp-GOL / | #5: 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: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.16M Calcium Acetate, 0.08 M Sodium Cacodylate, pH 6.5, 14.4% PEG8000, and 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→156.75 Å / Num. obs: 52278 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.73 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 2.27→2.39 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 7553 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KVN Resolution: 2.27→89.86 Å / Cor.coef. Fo:Fc: 0.9292 / Cor.coef. Fo:Fc free: 0.9208 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.185
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Displacement parameters | Biso mean: 42.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.258 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.27→89.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.33 Å / Total num. of bins used: 20
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