+Open data
-Basic information
Entry | Database: PDB / ID: 6tcs | |||||||||
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Title | Crystal structure of the omalizumab scFv | |||||||||
Components | Omalizumab scFv | |||||||||
Keywords | IMMUNE SYSTEM / Fab / Antibody / immunoglobulin | |||||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Mitropoulou, A.N. / Ceska, T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization. Authors: Mitropoulou, A.N. / Ceska, T. / Heads, J.T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tcs.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tcs.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/6tcs ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcs | HTTPS FTP |
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-Related structure data
Related structure data | 6tcmSC 6tcnC 6tcoC 6tcpC 6tcqC 6tcrC S: Starting model for refinement C: citing same article (ref.) |
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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: 29596.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Omalizumab scFv / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M tri-sodium citrate pH5.6, 15% PEG 4000 and 0.2M ammonium sulphate. Crystals were cryoprotected with 0.1M tri-sodium citrate pH5.6, 30% PEG 4000 and 0.2M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→64.01 Å / Num. obs: 17055 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 24.6 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.121 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.2 % / Rmerge(I) obs: 2.248 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1655 / CC1/2: 0.597 / Rpim(I) all: 1.064 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TCM Resolution: 2.3→56.237 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.85 Å2 / Biso mean: 33.9248 Å2 / Biso min: 11.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→56.237 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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