+Open data
-Basic information
Entry | Database: PDB / ID: 8oju | ||||||
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Title | Crystal structure of the human IgD Fab - structure Fab3 | ||||||
Components | (Human IgD Fab ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Fab / Antibody / Immunoglobulin | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Davies, A.M. / Beavil, R.L. / McDonnell, J.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol.Immunol. / Year: 2023 Title: Crystal structures of the human IgD Fab reveal insights into C H 1 domain diversity. Authors: Davies, A.M. / Beavil, R.L. / Barbolov, M. / Sandhar, B.S. / Gould, H.J. / Beavil, A.J. / Sutton, B.J. / McDonnell, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oju.cif.gz | 194.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oju.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 8oju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/8oju ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8oju | 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
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 22769.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVitro / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 25399.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVitro / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
-Non-polymers , 4 types, 397 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 6000 and 0.1M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→70.87 Å / Num. obs: 78636 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3890 / CC1/2: 0.462 / Rpim(I) all: 0.661 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→51.25 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.74 / 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: 1.45→51.25 Å
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Refine LS restraints |
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LS refinement shell |
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