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Yorodumi- PDB-5ijk: Crystal structure of anti-gliadin 1002-1E03 Fab fragment in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ijk | ||||||
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Title | Crystal structure of anti-gliadin 1002-1E03 Fab fragment in complex of peptide PLQPEQPFP | ||||||
Components |
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Keywords | IMMUNE SYSTEM / anti-gliadin antibody / celiac disease | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) Triticum aestivum (bread wheat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Snir, O. / Chen, X. / Gidoni, M. / du Pre, M.F. / Zhao, Y. / Steinsbo, O. / Lundin, K.E. / Yaari, G. / Sollid, L.M. | ||||||
Citation | Journal: JCI Insight / Year: 2017 Title: Stereotyped antibody responses target posttranslationally modified gluten in celiac disease. Authors: Snir, O. / Chen, X. / Gidoni, M. / du Pre, M.F. / Zhao, Y. / Steinsbo, O. / Lundin, K.E. / Yaari, G. / 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 | 5ijk.cif.gz | 352.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ijk.ent.gz | 287.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ijk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ijk_validation.pdf.gz | 492.1 KB | Display | wwPDB validaton report |
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Full document | 5ijk_full_validation.pdf.gz | 506 KB | Display | |
Data in XML | 5ijk_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 5ijk_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/5ijk ftp://data.pdbj.org/pub/pdb/validation_reports/ij/5ijk | HTTPS FTP |
-Related structure data
Related structure data | 5ifjC 5ig7C 5ihzSC 5ik3C 5it2S C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1052.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Triticum aestivum (bread wheat) #2: Antibody | Mass: 24137.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 24326.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.88 Å3/Da / Density % sol: 57.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.256M (NH4)2SO4, 0.1M Citrate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.29 Å / Num. obs: 39676 / % possible obs: 99.9 % / Redundancy: 8.8 % / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.5→2.6 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IHZ, 5IT2 Resolution: 2.5→47.29 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.29 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: -1.4087 Å / Origin y: -32.7301 Å / Origin z: 25.3417 Å
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Refinement TLS group | Selection details: ALL |