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Yorodumi- PDB-6h2y: human Fab 1E6 bound to fHbp variant 3 from Neisseria meningitidis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2y | ||||||
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Title | human Fab 1E6 bound to fHbp variant 3 from Neisseria meningitidis serogroup B | ||||||
Components |
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Keywords | IMMUNE SYSTEM / fHbp / Human Fab / Neisseria / Antigen-antibody Complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Veggi, D. / Bianchi, F. / Cozzi, R. / Malito, E. / Bottomley, M.J. | ||||||
Citation | Journal: Faseb J. / Year: 2019 Title: Cocrystal structure of meningococcal factor H binding protein variant 3 reveals a new crossprotective epitope recognized by human mAb 1E6. Authors: Bianchi, F. / Veggi, D. / Santini, L. / Buricchi, F. / Bartolini, E. / Lo Surdo, P. / Martinelli, M. / Finco, O. / Masignani, V. / Bottomley, M.J. / Maione, D. / Cozzi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h2y.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h2y.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 6h2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h2y_validation.pdf.gz | 709.9 KB | Display | wwPDB validaton report |
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Full document | 6h2y_full_validation.pdf.gz | 724.5 KB | Display | |
Data in XML | 6h2y_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 6h2y_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2y ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2y | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules D
#1: Protein | Mass: 29969.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna1870 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q19KF7 |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23559.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23098.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Non-polymers , 5 types, 89 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-P33 / | #7: Chemical | ChemComp-PG4 / | #8: 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: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Molecular Dimensions Morpheus HT-96 screen, well D9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.983 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→65.28 Å / Num. obs: 23201 / % possible obs: 97.7 % / Redundancy: 4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.159 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3370 / CC1/2: 0.472 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→63.561 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→63.561 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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