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- PDB-7n3a: Crystal structure of 9-site deamidated variant of human gamma(S)-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n3a | ||||||
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Title | Crystal structure of 9-site deamidated variant of human gamma(S)-crystallin | ||||||
![]() | Gamma-crystallin S | ||||||
![]() | STRUCTURAL PROTEIN / crystallin / human crystallin / gamma(S) crystallin / eye lens protein | ||||||
Function / homology | ![]() structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Norton-Baker, B. / Mehrabi, P. / Martin, R.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.2 KB | Display | ![]() |
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Full document | ![]() | 424.1 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n36C ![]() 7n37C ![]() 7n38C ![]() 7n39C ![]() 7n3bC ![]() 6fd8S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20968.500 Da / Num. of mol.: 1 / Mutation: N15D,Q17E,N54D,Q64E,Q71E,Q93E,Q107E,Q121E,N144D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH 5.45, 21% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.74 Å / Num. obs: 23517 / % possible obs: 98.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.85 |
Reflection shell | Resolution: 1.5→1.55 Å / Num. unique obs: 2292 / CC1/2: 0.734 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FD8 Resolution: 1.5→43.74 Å / SU ML: 0.2225 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.7047 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: 36.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→43.74 Å
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Refine LS restraints |
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LS refinement shell |
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