+Open data
-Basic information
Entry | Database: PDB / ID: 2xa8 | ||||||
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Title | Crystal structure of the Fab domain of omalizumab at 2.41A | ||||||
Components |
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Keywords | IMMUNE SYSTEM / XOLAIR / ALLERGY | ||||||
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: 2.42 Å | ||||||
Authors | Huang, C.H. / Hung, F.H.A. / Lim, C. / Chang, T.W. / Ma, C. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural and Physical Basis for Anti-IgE Therapy. Authors: Wright, J.D. / Chu, H.M. / Huang, C.H. / Ma, C. / Chang, T.W. / Lim, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xa8.cif.gz | 177.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xa8.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xa8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xa8_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 2xa8_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 2xa8_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 2xa8_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/2xa8 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xa8 | HTTPS FTP |
-Related structure data
Related structure data | 2vl5S S: Starting model for refinement |
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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
#1: Antibody | Mass: 23297.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) |
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#2: Antibody | Mass: 23922.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0 M AMMONIUM SULFATE, 0.1 M NA HEPES PH 7.5, 2% W/V PEG400. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 |
Detector | Type: BRUKER / Detector: CCD / Date: Jan 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→30 Å / Num. obs: 25869 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.43 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VL5 Resolution: 2.42→36.93 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.9 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.55 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→36.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 60.5155 Å / Origin y: 40.2083 Å / Origin z: 16.6056 Å
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Refinement TLS group | Selection details: ALL |