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Yorodumi- PDB-8qyb: J22.9-ISY, fully humanized and CDR optimized Fab Fragment based o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qyb | |||||||||
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Title | J22.9-ISY, fully humanized and CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment / humanized / BCMA binding | |||||||||
Function / homology | Function and homology information lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | |||||||||
Authors | Marino, S.F. / Daumke, O. | |||||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure-based humanization of a therapeutic antibody for Multiple Myeloma Authors: Marino, S.F. / Daumke, O. #1: Journal: Mol Oncol / Year: 2015 Title: Potent anti-tumor response by targeting B cell maturation antigen (BCMA) in a mouse model of multiple myeloma. Authors: Marino, S.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qyb.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qyb.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 8qyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qyb_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 8qyb_full_validation.pdf.gz | 435.7 KB | Display | |
Data in XML | 8qyb_validation.xml.gz | 17 KB | Display | |
Data in CIF | 8qyb_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/8qyb ftp://data.pdbj.org/pub/pdb/validation_reports/qy/8qyb | HTTPS FTP |
-Related structure data
Related structure data | 8qy9C 8qyaC C: citing same article (ref.) |
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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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Unit cell |
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-Components
#1: Antibody | Mass: 23048.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 293_6E / Production host: Homo sapiens (human) | ||
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#2: Antibody | Mass: 23558.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 203_8E / Production host: Homo sapiens (human) | ||
#3: Protein/peptide | Mass: 3783.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF17, BCM, BCMA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02223 | ||
#4: Chemical | 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: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG 3350 7.5 mM CuCl2 BisTris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→45.25 Å / Num. obs: 9514 / % possible obs: 98.96 % / Redundancy: 3.6 % / Biso Wilson estimate: 63.36 Å2 / CC1/2: 0.975 / Rrim(I) all: 0.25 / Net I/σ(I): 5.15 |
Reflection shell | Resolution: 3.09→3.205 Å / Num. unique obs: 1380 / CC1/2: 0.728 / Rrim(I) all: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→45.25 Å / SU ML: 0.469 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.1473 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: 62.73 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→45.25 Å
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Refine LS restraints |
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LS refinement shell |
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