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Yorodumi- PDB-4lxg: Crystal structure of DxnB2, a carbon - carbon bond hydrolase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lxg | ||||||
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Title | Crystal structure of DxnB2, a carbon - carbon bond hydrolase from Sphingomonas wittichii RW1 | ||||||
Components | MCP Hydrolase | ||||||
Keywords | HYDROLASE / Carbon-carbon bond hydrolase / Rossmann Fold / alpha/beta hydrolase fold / Cytosolic | ||||||
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 Function and homology information | ||||||
Biological species | Sphingomonas wittichii RW1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å | ||||||
Authors | Bhowmik, S. / Bolin, J.T. | ||||||
Citation | Journal: Biochemistry / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lxg.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lxg.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/4lxg ftp://data.pdbj.org/pub/pdb/validation_reports/lx/4lxg | HTTPS FTP |
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-Related structure data
Related structure data | 4lxhC 4lydC 1j1iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30224.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas wittichii RW1 (bacteria) / Strain: RW1 / Gene: dxnB2, Swit_3055 / Production host: Escherichia coli (E. coli) References: UniProt: A5VAT9, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase | ||
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#2: Chemical | #3: 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: 3.47 Å3/Da / Density % sol: 64.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.2 Details: grid of ammonium sulfate (1.0-2.5 M) containing 0.1 M Tris, pH 8.2 and 6-10% ethanol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→58.03 Å / Num. all: 22668 / Num. obs: 22668 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.2→2.2 Å / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J1I Resolution: 2.22→36.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.378 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.64 Å2 / Biso mean: 52.9638 Å2 / Biso min: 31.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→36.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.223→2.281 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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