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Yorodumi- PDB-7n38: Crystal structure of 5-site deamidated variant of human gamma(S)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n38 | ||||||
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Title | Crystal structure of 5-site deamidated variant of human gamma(S)-crystallin | ||||||
Components | Gamma-crystallin S | ||||||
Keywords | STRUCTURAL PROTEIN / crystallin / human crystallin / gamma(S) crystallin / eye lens protein | ||||||
Function / homology | Function and homology information structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Norton-Baker, B. / Mehrabi, P. / Martin, R.W. | ||||||
Citation | Journal: Structure / Year: 2022 Title: Deamidation of the human eye lens protein gamma S-crystallin accelerates oxidative aging. Authors: Norton-Baker, B. / Mehrabi, P. / Kwok, A.O. / Roskamp, K.W. / Rocha, M.A. / Sprague-Piercy, M.A. / von Stetten, D. / Miller, R.J.D. / Martin, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n38.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n38.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 7n38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/7n38 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/7n38 | HTTPS FTP |
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-Related structure data
Related structure data | 7n36C 7n37C 7n39C 7n3aC 7n3bC 6fd8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20964.559 Da / Num. of mol.: 1 / Mutation: N15D,N54D,Q93E,Q121E,N144D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8 / Production host: Escherichia coli (E. coli) / References: UniProt: P22914 |
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#2: Chemical | ChemComp-BTB / |
#3: Chemical | ChemComp-MG / |
#4: 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: 1.75 Å3/Da / Density % sol: 29.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M MgCl2, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→39.9 Å / Num. obs: 41328 / % possible obs: 93.52 % / Redundancy: 12.8 % / Biso Wilson estimate: 15.58 Å2 / CC1/2: 1 / Net I/σ(I): 30.24 |
Reflection shell | Resolution: 1.22→1.27 Å / Num. unique obs: 2350 / CC1/2: 0.715 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FD8 Resolution: 1.22→39.9 Å / SU ML: 0.1098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6966 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→39.9 Å
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Refine LS restraints |
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LS refinement shell |
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