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Yorodumi- PDB-4fd9: Crystal structure of the third beta-gamma-crystallin domain of Cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fd9 | ||||||
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Title | Crystal structure of the third beta-gamma-crystallin domain of Crybg3 (betagamma-crystallin domain-containing protein 3) from Mus musculus | ||||||
Components | Beta/gamma crystallin domain-containing protein 3 | ||||||
Keywords | STRUCTURAL PROTEIN / Non-lens vertebrate beta-gamma-crystallin / Brain | ||||||
Function / homology | Function and homology information structural constituent of eye lens / lens development in camera-type eye / protein kinase A binding / visual perception / carbohydrate binding / protein-containing complex Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Aravind, P. / Srivastava, S.S. / Sankaranarayanan, R. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Aggregation-prone near-native intermediate formation during unfolding of a structurally similar nonlenticular beta/gamma-crystallin domain Authors: Rajanikanth, V. / Srivastava, S.S. / Singh, A.K. / Rajyalakshmi, M. / Chandra, K. / Aravind, P. / Sankaranarayanan, R. / Sharma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fd9.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fd9.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/4fd9 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fd9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-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: 10434.805 Da / Num. of mol.: 2 / Fragment: beta-gamma-crystallin domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Tissue: Brain / Gene: Crybg3 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q80W49 #2: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-25% PEG 4K, 0.1M Na Hepes, 10% isopropanol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2007 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.86→25 Å / Num. obs: 13629 / Redundancy: 5.7 % / Rmerge(I) obs: 0.037 | |||||||||||||||
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 5 % / Rmerge(I) obs: 0.2 / Num. unique all: 1167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→22.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.774 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 24.189 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→22.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.865→1.913 Å / Total num. of bins used: 20
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