+Open data
-Basic information
Entry | Database: PDB / ID: 6ana | |||||||||
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Title | LL2 Fab in complex with anti-Kappa VHH domain | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / antibody / CD22 / VHH domain | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Lama glama (llama) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | |||||||||
Authors | Sicard, T. / Ereno Orbea, J. / 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 | 6ana.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ana.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ana.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ana_validation.pdf.gz | 759.3 KB | Display | wwPDB validaton report |
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Full document | 6ana_full_validation.pdf.gz | 761.2 KB | Display | |
Data in XML | 6ana_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 6ana_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/6ana ftp://data.pdbj.org/pub/pdb/validation_reports/an/6ana | HTTPS FTP |
-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: 10400.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 23701.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 24121.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
Sequence details | Anti-kappa VHH domain is represented as poly-UNK. The side chains were not included in the refinement. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 1M lithium chloride 0.1M MES, pH 6.0 |
-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: Sep 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.559 Å / Num. obs: 58574 / % possible obs: 89.6 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.036 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.7→1.72 Å / Rmerge(I) obs: 0.362 / CC1/2: 0.765 / Rpim(I) all: 0.258 |
-Processing
Software |
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Refinement | Resolution: 1.7→38.559 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.41 / 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: 1.7→38.559 Å
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Refine LS restraints |
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LS refinement shell |
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