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Yorodumi- PDB-8bd0: Human Gamma-D crystallin R36S mutant with DTT-Cystein Protein mod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bd0 | ||||||
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Title | Human Gamma-D crystallin R36S mutant with DTT-Cystein Protein modification | ||||||
Components | Human Gamma-D Crystallin R36S | ||||||
Keywords | STRUCTURAL PROTEIN / chemical modification / oxidisation / eye lens protein | ||||||
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: 2 Å | ||||||
Authors | Yorke, B.A. / Hill, J.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Commun Chem / Year: 2024 Title: An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin. Authors: Hill, J.A. / Nyathi, Y. / Horrell, S. / von Stetten, D. / Axford, D. / Owen, R.L. / Beddard, G.S. / Pearson, A.R. / Ginn, H.M. / Yorke, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bd0.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bd0.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 8bd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/8bd0 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/8bd0 | HTTPS FTP |
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-Related structure data
Related structure data | 2g98S S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20346.600 Da / Num. of mol.: 2 / Mutation: R36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30b(+) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P07320 #2: Chemical | ChemComp-DTT / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.8 Å3/Da / Density % sol: 56.07 % / Description: microcrystalline plate-like |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 7.8 / Details: 50 mM phosphate buffer pH 7.8, 20 mM DTT / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→101.13 Å / Num. obs: 31629 / % possible obs: 99.99 % / Redundancy: 50.3 % / CC1/2: 0.9956 / CC star: 0.982 / R split: 0.2717 / Net I/σ(I): 2.71 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 34.7 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3090 / CC1/2: 0.14 / CC star: 0.5062 / R split: 1.94 / % possible all: 100 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography data reduction | Frames indexed: 25600 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G98 Resolution: 2→101 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.358 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.637 Å2
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Refinement step | Cycle: 1 / Resolution: 2→101 Å
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