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Yorodumi- PDB-5aze: Fab fragment of calcium-dependent antigen binding antibody, 6RL#9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aze | |||||||||
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Title | Fab fragment of calcium-dependent antigen binding antibody, 6RL#9 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / calcium-dependent / RECYCLING ANTIBODY | |||||||||
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 | Kadono, S. / Hironiwa, N. / Ishii, S. / Igawa, T. / Hattori, K. | |||||||||
Citation | Journal: Mabs / Year: 2016 Title: Calcium-dependent antigen binding as a novel modality for antibody recycling by endosomal antigen dissociation Authors: Hironiwa, N. / Ishii, S. / Kadono, S. / Iwayanagi, Y. / Mimoto, F. / Habu, K. / Igawa, T. / Hattori, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aze.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aze.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 5aze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/5aze ftp://data.pdbj.org/pub/pdb/validation_reports/az/5aze | 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: 22789.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24432.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20.0% PEG 4000, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.35 Å / Num. obs: 22199 / % possible obs: 99.99 % / Observed criterion σ(I): -3 / Redundancy: 7.12 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.25 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZA6 for VH, CL, and CH1 regions, 2A9M for VL region Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 6.947 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.33 Å2 / Biso mean: 27.373 Å2 / Biso min: 17.06 Å2
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Refinement step | Cycle: final / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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