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Yorodumi- PDB-7lcv: Factor H enhancing human antibody fragment (Fab) to meningococcal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lcv | ||||||
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Title | Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human / antibody / Fab / meningococcal vaccine / Factor H binding protein / complex | ||||||
Function / homology | : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Factor H binding protein variant B24 Function and homology information | ||||||
Biological species | Homo sapiens (human) Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Beernink, P.T. / Sands, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2021 Title: Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site. Authors: Sands, N.A. / Beernink, P.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lcv.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lcv.ent.gz | 191.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lcv_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 7lcv_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 7lcv_validation.xml.gz | 27 KB | Display | |
Data in CIF | 7lcv_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/7lcv ftp://data.pdbj.org/pub/pdb/validation_reports/lc/7lcv | HTTPS FTP |
-Related structure data
Related structure data | 7ke1C 7ketC 3cvdS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23978.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) | ||||
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#2: Antibody | Mass: 23565.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) | ||||
#3: Protein | Mass: 28074.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: fhbp / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VRZ6 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M LiNO3, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→81.18 Å / Num. obs: 65915 / % possible obs: 93.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.68 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 11.59 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6477 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.513 / Rrim(I) all: 0.983 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CVD and Fab homology model Resolution: 1.7→81.18 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.8457 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→81.18 Å
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Refine LS restraints |
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LS refinement shell |
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