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- PDB-4lyd: Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lyd | ||||||
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Title | Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1 | ||||||
![]() | MCP Hydrolase | ||||||
![]() | HYDROLASE / meta-cleavage product hydrolase / C-C bond hydrolase / alpha-beta hydrolase / dibenzo-p-dioxin degradation / dibenzofuran degradation | ||||||
Function / homology | Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Alpha/beta hydrolase fold![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ghosh, S. / Bolin, J.T. / Bhowmik, S. | ||||||
![]() | ![]() Title: The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites. Authors: Ruzzini, A.C. / Bhowmik, S. / Yam, K.C. / Ghosh, S. / Bolin, J.T. / Eltis, L.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.5 KB | Display | ![]() |
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PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30208.531 Da / Num. of mol.: 1 / Mutation: S105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A5VAT9, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.5 M sodium malonate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 20422 / % possible obs: 93.5 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.078 / Χ2: 1.206 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 39.22 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 104.57 Å2 / Biso mean: 47.9948 Å2 / Biso min: 27.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→43.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.256→2.315 Å / Total num. of bins used: 20
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