+Open data
-Basic information
Entry | Database: PDB / ID: 6ani | ||||||
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Title | Coltuximab Fab in complex with anti-Kappa VHH domain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / antibody / CD19 / VHH domain | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Lama glama (llama) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Ereno Orbea, J. / Sicard, T. / Julien, J.-P. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments. Authors: Ereno-Orbea, J. / Sicard, T. / Cui, H. / Carson, J. / Hermans, P. / Julien, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ani.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ani.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ani.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/6ani ftp://data.pdbj.org/pub/pdb/validation_reports/an/6ani | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 10315.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) #2: Antibody | Mass: 23840.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23041.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | Anti-kappa VHH domain is represented as poly-UNK. The side chains were not included in the refinement. | |
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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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.0 and 14 % polyethyleneglycol (PEG) 3350 (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.596 Å / Num. obs: 43226 / % possible obs: 99.4 % / Redundancy: 4.33 % / Biso Wilson estimate: 36.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.074 / Net I/σ(I): 9.18 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.683 / Num. measured obs: 27663 / CC1/2: 0.583 / Rpim(I) all: 0.372 |
-Processing
Software |
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Refinement | Resolution: 2.4→46.6 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.6 Å
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Refine LS restraints |
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LS refinement shell |
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