+Open data
-Basic information
Entry | Database: PDB / ID: 8bpi | ||||||
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Title | Human Gamma-D crystallin R36S mutant after UV illumination | ||||||
Components | (Gamma-crystallin D) x 2 | ||||||
Keywords | STRUCTURAL PROTEIN / UV exposure / 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: To Be Published Title: Human Gamma-D crystallin R36S mutant with DTT-Protein modification Authors: Yorke, B.Y. / Hill, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bpi.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bpi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpi ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpi | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 172 / Label seq-ID: 10 - 181
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 21814.240 Da / Num. of mol.: 1 / Mutation: R36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Plasmid: pET30b(+) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P07320 |
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#2: Protein | Mass: 21830.240 Da / Num. of mol.: 1 / Mutation: R36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Plasmid: pET30b(+) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P07320 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / 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 16M / 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 Å / Num. obs: 31633 / % possible obs: 100 % / Redundancy: 70.2 % / CC1/2: 0.9546 / CC star: 0.9883 / R split: 0.2277 / Net I/σ(I): 3.19 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 48.3 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 3090 / CC1/2: 0.2283 / CC star: 0.6096 / R split: 1.669 / % 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: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.722 / SU ML: 0.164 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.179 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.112 Å2
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Refinement step | Cycle: LAST / Resolution: 2→101 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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