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Yorodumi- PDB-3giz: Crystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab -
+Open data
-Basic information
Entry | Database: PDB / ID: 3giz | ||||||
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Title | Crystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CD20 / 2F2 / Ofatumumab / Hu-MaxCD20 / Fab / antibody / fully human antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Du, J. / Yang, H. / Ding, J. | ||||||
Citation | Journal: Mol.Immunol. / Year: 2009 Title: Structure of the Fab fragment of therapeutic antibody Ofatumumab provides insights into the recognition mechanism with CD20 Authors: Du, J. / Yang, H. / Guo, Y. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3giz.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3giz.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 3giz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3giz_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 3giz_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 3giz_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3giz_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3giz ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3giz | HTTPS FTP |
-Related structure data
Related structure data | 1u6aS 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 23174.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): ovary (CHO) cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1 | ||
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#2: Antibody | Mass: 23717.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): ovary (CHO) cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.2 M zinc acetate, 20% PEG3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 26208 / Num. obs: 26051 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2618 / Rsym value: 0.325 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U6A Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.528 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.506 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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