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Yorodumi- PDB-5bvj: The molecular mode of action and species specificity of canakinum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bvj | |||||||||
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Title | The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / Fab | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Rondeau, J.M. | |||||||||
Citation | Journal: Mabs / Year: 2015 Title: The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1 beta. Authors: Rondeau, J.M. / Ramage, P. / Zurini, M. / Gram, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bvj.cif.gz | 357.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bvj.ent.gz | 298.7 KB | Display | PDB format |
PDBx/mmJSON format | 5bvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bvj_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 5bvj_full_validation.pdf.gz | 486.7 KB | Display | |
Data in XML | 5bvj_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 5bvj_validation.cif.gz | 106 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/5bvj ftp://data.pdbj.org/pub/pdb/validation_reports/bv/5bvj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23381.908 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): myeloma / Cell line (production host): SP2/0 / Production host: Mus musculus (house mouse) #2: Antibody | Mass: 24179.053 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SP2/0 / Production host: Mus musculus (house mouse) #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: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 12% PEG MME 5000, 50mM sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 1, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→100 Å / Num. obs: 114298 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.952 / Net I/av σ(I): 27.517 / Net I/σ(I): 11.7 / Num. measured all: 552811 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 25643448 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7882 Å2 / ksol: 0.3406 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.84 Å2 / Biso mean: 25 Å2 / Biso min: 6.25 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 2→50.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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