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- PDB-4h7i: Crystal structure of haloalkane dehalogenase LinB L138I mutant fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h7i | ||||||
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Title | Crystal structure of haloalkane dehalogenase LinB L138I mutant from Sphingobium sp. MI1205 | ||||||
![]() | Haloalkane dehalogenase | ||||||
![]() | HYDROLASE / alpha/beta hydrolase fold | ||||||
Function / homology | ![]() haloalkane dehalogenase / haloalkane dehalogenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okai, M. / Ohtsuka, J. / Imai, L.F. / Mase, T. / Moriuchi, R. / Tsuda, M. / Nagata, K. / Nagata, Y. / Tanokura, M. | ||||||
![]() | ![]() Title: Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205. Authors: Okai, M. / Ohtsuka, J. / Imai, L.F. / Mase, T. / Moriuchi, R. / Tsuda, M. / Nagata, K. / Nagata, Y. / Tanokura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.4 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.2 KB | Display | ![]() |
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Full document | ![]() | 429.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h77SC ![]() 4h7dC ![]() 4h7eC ![]() 4h7fC ![]() 4h7hC ![]() 4h7jC ![]() 4h7kC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34096.586 Da / Num. of mol.: 1 / Mutation: L138I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.74 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Date: Jun 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 25640 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H77 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.161 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.114 / 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: 13.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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