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Yorodumi- PDB-3sny: Crystal structure of a mutant T82R of a betagamma-crystallin doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sny | ||||||
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Title | Crystal structure of a mutant T82R of a betagamma-crystallin domain from Clostridium beijerinckii | ||||||
Components | Clostrillin | ||||||
Keywords | METAL BINDING PROTEIN / calcium-bound betagamma-crystallin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium beijerinckii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Srivastava, S.S. / Sankaranarayanan, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Decoding the molecular design principles underlying Ca(2+) binding to beta gamma-crystallin motifs Authors: Mishra, A. / Suman, S.K. / Srivastava, S.S. / 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 | 3sny.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sny.ent.gz | 21.8 KB | Display | PDB format |
PDBx/mmJSON format | 3sny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/3sny ftp://data.pdbj.org/pub/pdb/validation_reports/sn/3sny | HTTPS FTP |
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-Related structure data
Related structure data | 3snzC 3so0C 3so1C 3i9hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10749.718 Da / Num. of mol.: 1 / Fragment: betagamma-crystallin domain, UNP residues 118-213 / Mutation: T82R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Strain: NCIMB 8052 / Gene: Cbei_2825 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6LX94 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | #4: 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: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 25-30% PEG 3350, 0.1M HEPES, 0.1-0.2M lithium sulphate, pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 9, 2010 / Details: VariMax optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 10242 / Redundancy: 13.3 % / Rsym value: 0.029 / Net I/σ(I): 84.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 31.8 / Rsym value: 0.081 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I9H Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.318 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.046 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.899 Å / Total num. of bins used: 20
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