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Yorodumi- PDB-5it2: Structure of a transglutaminase 2-specific autoantibody 693-10-B0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5it2 | ||||||
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Title | Structure of a transglutaminase 2-specific autoantibody 693-10-B06 Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Transglutaminase 2 / autoantibody / Fab fragment | ||||||
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: 1.7 Å | ||||||
Authors | Chen, X. / Dalhus, B. / Hnida, K. / Iversen, R. / Sollid, L.M. | ||||||
Citation | Journal: Nat. Med. / Year: 2012 Title: High abundance of plasma cells secreting transglutaminase 2-specific IgA autoantibodies with limited somatic hypermutation in celiac disease intestinal lesions Authors: Di Niro, R. / Mesin, L. / Zheng, N.Y. / Stamnaes, J. / Morrissey, M. / Lee, J.H. / Huang, M. / Iversen, R. / du Pre, M.F. / Qiao, S.W. / Lundin, K.E. / Wilson, P.C. / Sollid, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5it2.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5it2.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 5it2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5it2 ftp://data.pdbj.org/pub/pdb/validation_reports/it/5it2 | HTTPS FTP |
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-Related structure data
Related structure data | 4zd3S 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: 24363.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23526.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: 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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris, pH=8.5, 20%v/v Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→54.24 Å / Num. obs: 54158 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZD3 Resolution: 1.7→43.867 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.7→43.867 Å
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LS refinement shell | Resolution: 1.7→1.7293 Å / Total num. of bins used: 20
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