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Yorodumi- PDB-8bk2: X-ray structure of meningococcal factor H binding protein variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bk2 | ||||||
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Title | X-ray structure of meningococcal factor H binding protein variant 2 in complex with a specific and bactericidal human monoclonal antibody 1B1 | ||||||
Components |
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Keywords | PROTEIN BINDING / Meningococcus / Antigen / Human Monoclonal / fHbp / Bactericidal / Factor H displacement / Vaccine. | ||||||
Function / homology | Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / IMIDAZOLE / Factor H-binding protein Function and homology information | ||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Veggi, D. / Bottomley, J.M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Bactericidal human monoclonal antibody 1B1 specific for meningococcal factor H binding protein variant 2 and displaces human factor H Authors: Veggi, D. / Bottomley, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bk2.cif.gz | 390.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bk2.ent.gz | 286.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bk2_validation.pdf.gz | 954.1 KB | Display | wwPDB validaton report |
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Full document | 8bk2_full_validation.pdf.gz | 1001.5 KB | Display | |
Data in XML | 8bk2_validation.xml.gz | 69.7 KB | Display | |
Data in CIF | 8bk2_validation.cif.gz | 94.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/8bk2 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/8bk2 | HTTPS FTP |
-Related structure data
Related structure data | 6xzwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 28217.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Gene: fhbp / Production host: Escherichia coli (E. coli) / References: UniProt: B9VX96 |
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-Antibody , 2 types, 6 molecules HDFLEG
#2: Antibody | Mass: 23871.760 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23513.143 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Non-polymers , 7 types, 224 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-IMD / | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-P33 / | #8: Chemical | ChemComp-MPD / ( | #9: Chemical | ChemComp-P6G / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.09M Sodium Nitrate, Sodium Phosphate dibasic, Ammonium Solphate, 0.1 M Buffer Imidazole, MES monohydrate, pH6.5 and as precipitant mix 25% v/v MPD, 25% PEG 100, 25% w/v PEG 3350. |
-Data collection
Diffraction | Mean temperature: 150 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→49.66 Å / Num. obs: 92813 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 62.03 Å2 / CC1/2: 0.997 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.41→2.49 Å / Num. unique obs: 9128 / CC1/2: 0.494 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XZW Resolution: 2.41→49.66 Å / SU ML: 0.4322 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5397 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→49.66 Å
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Refine LS restraints |
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LS refinement shell |
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