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Yorodumi- PDB-4ub0: New design for monovalent bispecific IgG through cysteine enginee... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ub0 | ||||||
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Title | New design for monovalent bispecific IgG through cysteine engineering of the CH1-CL interface | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / knobs-into-holes / bispecific | ||||||
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: 2.2 Å | ||||||
Authors | Oganesyan, V.Y. / Dall'Acqua, W.F. | ||||||
Citation | Journal: Mabs / Year: 2015 Title: Improving target cell specificity using a novel monovalent bispecific IgG design. Authors: Mazor, Y. / Oganesyan, V. / Yang, C. / Hansen, A. / Wang, J. / Liu, H. / Sachsenmeier, K. / Carlson, M. / Gadre, D.V. / Borrok, M.J. / Yu, X.Q. / Dall'Acqua, W. / Wu, H. / Chowdhury, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ub0.cif.gz | 176.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ub0.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ub0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ub0_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 4ub0_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 4ub0_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4ub0_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/4ub0 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/4ub0 | 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
#1: Antibody | Mass: 23381.148 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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#2: Antibody | Mass: 23466.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: protein @ 19 mg/ml in 10 mM Tris-HCl, pH 8.0, 100 mM NaCl; 0.018 M of each of the following salt solutions: CaCl2, CoCl2, and CdCl2; 18% PEG 3350 and 5% glycerol PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97931 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→53.6 Å / Num. obs: 25434 / % possible obs: 97.4 % / Redundancy: 3.8 % / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.2→2.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.8 / % possible all: 97.9 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→53.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU B: 19.377 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.35 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→53.6 Å
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