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Yorodumi- PDB-6p9i: crystal structure of human anti staphylococcus aureus antibody ST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p9i | ||||||
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Title | crystal structure of human anti staphylococcus aureus antibody STAU-399 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human antibody / Fab | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Dong, J. / Crowe, J.E. | ||||||
Citation | Journal: Mbio / Year: 2019 Title: Human V H 1-69 Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis. Authors: Bennett, M.R. / Dong, J. / Bombardi, R.G. / Soto, C. / Parrington, H.M. / Nargi, R.S. / Schoeder, C.T. / Nagel, M.B. / Schey, K.L. / Meiler, J. / Skaar, E.P. / Crowe Jr., J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p9i.cif.gz | 338.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p9i.ent.gz | 274.2 KB | Display | PDB format |
PDBx/mmJSON format | 6p9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p9i_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 6p9i_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 6p9i_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 6p9i_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/6p9i ftp://data.pdbj.org/pub/pdb/validation_reports/p9/6p9i | HTTPS FTP |
-Related structure data
Related structure data | 6p9hC 6p9jC 5jrpS 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
#1: Antibody | Mass: 24130.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23129.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: 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: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 10% PEG 200, 18% PEG 8000, 0.1 M Bis-tris propane pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.29 Å / Num. obs: 35657 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.581 / Num. unique obs: 5197 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JRP Resolution: 2.4→45.71 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.4198 Å / Origin y: -10.6392 Å / Origin z: 22.4723 Å
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Refinement TLS group | Selection details: all |