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- PDB-3so0: Crystal structure of a mutant T41S of a betagamma-crystallin doma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3so0 | ||||||
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Title | Crystal structure of a mutant T41S of a betagamma-crystallin domain from Clostridium beijerinckii | ||||||
![]() | Clostrillin | ||||||
![]() | METAL BINDING PROTEIN / calcium-bound betagamma-crystallin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Srivastava, S.S. / Sankaranarayanan, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.3 KB | Display | ![]() |
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PDB format | ![]() | 118.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.6 KB | Display | ![]() |
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Full document | ![]() | 490.9 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3snyC ![]() 3snzC ![]() 3so1C ![]() 3i9hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10679.602 Da / Num. of mol.: 8 / Fragment: betagamma-crystallin domain, UNP residues 118-213 / Mutation: T41S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.717916 Å3/Da / Density % sol: 28.401621 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 25-30% PEG 3350, 0.1M HEPES, 0.1-0.2M lithium sulphate, pH 7.0-7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 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: 1.93→50 Å / Num. obs: 44875 / Redundancy: 4.2 % / Rsym value: 0.099 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.459 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3I9H Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.038 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.171 / 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: 21.262 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.931→1.981 Å / Total num. of bins used: 20
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