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Yorodumi- PDB-7p53: Crystal Structure of Human gamma-D-crystallin mutant C110M at 1.5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p53 | ||||||
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Title | Crystal Structure of Human gamma-D-crystallin mutant C110M at 1.57 Angstroms resolution | ||||||
Components | Gamma-crystallin D | ||||||
Keywords | STRUCTURAL PROTEIN / Cysteine mutation / Recombinant / Eye lens | ||||||
Function / homology | Function and homology information lens fiber cell differentiation / structural constituent of eye lens / lens development in camera-type eye / visual perception / cellular response to reactive oxygen species / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Strofaldi, A. / Khan, A.R. / McManus, J. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Surface Exposed Free Cysteine Suppresses Crystallization of Human gamma D-Crystallin. Authors: Strofaldi, A. / Khan, A.R. / McManus, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p53.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p53.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/7p53 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/7p53 | HTTPS FTP |
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-Related structure data
Related structure data | 1hk0S 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: Protein | Mass: 20663.021 Da / Num. of mol.: 1 / Mutation: C110M Source method: isolated from a genetically manipulated source Details: The protein is a mutant of Human gamma-D crystallin where the 110th cysteine is replaced by a methionine (C110M). Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Organ: Eye / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21-Gold(DE3) / References: UniProt: P07320 |
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#2: 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: 2.05 Å3/Da / Density % sol: 40 % / Description: Rhombic crystals. |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 7 Details: Crystals were obtained in 0.1M Sodium Phosphate Buffer pH 7 inducing LLPS at approximately 263K for 3hours from 150mg/mL solutions. Crystals were observed after few hours of incubation at 277K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→52.84 Å / Num. obs: 22817 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.083 / Rrim(I) all: 0.206 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.941 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 953 / Rpim(I) all: 0.883 / Rrim(I) all: 2.141 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hk0 Resolution: 1.57→45.51 Å / SU ML: 0.3044 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.562 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: 32.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→45.51 Å
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Refine LS restraints |
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LS refinement shell |
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