[English] 日本語
Yorodumi- PDB-8qya: J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qya | ||||||
---|---|---|---|---|---|---|---|
Title | J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA; with VH CDR2 glycosylation | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Fab fragment / humanized / CDR derivatized / BCMA binding | ||||||
Function / homology | COPPER (II) ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Marino, S.F. / Daumke, O. | ||||||
Funding support | 1items
| ||||||
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. / Damke, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qya.cif.gz | 316.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qya.ent.gz | 219.8 KB | Display | PDB format |
PDBx/mmJSON format | 8qya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qya_validation.pdf.gz | 744.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qya_full_validation.pdf.gz | 748.2 KB | Display | |
Data in XML | 8qya_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 8qya_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/8qya ftp://data.pdbj.org/pub/pdb/validation_reports/qy/8qya | HTTPS FTP |
-Related structure data
Related structure data | 8qy9C 8qybC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23321.840 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) |
---|---|
#2: Antibody | Mass: 23141.846 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) |
-Protein/peptide / Sugars , 2 types, 2 molecules A
#3: Protein/peptide | Mass: 3613.128 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) |
---|---|
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 22 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350 CuCl2 BisTris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / 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: 2.72→21.76 Å / Num. obs: 13486 / % possible obs: 99.42 % / Redundancy: 3.6 % / Biso Wilson estimate: 49.72 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.98 |
Reflection shell | Resolution: 2.72→2.817 Å / Num. unique obs: 1323 / CC1/2: 0.747 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→21.76 Å / SU ML: 0.4844 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.9191 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→21.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|