+Open data
-Basic information
Entry | Database: PDB / ID: 4whb | ||||||
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Title | Crystal structure of phenylurea hydrolase B | ||||||
Components | Phenylurea hydrolase B | ||||||
Keywords | HYDROLASE / Amidohydrolase / diuron hydrolase | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium brisbanense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.958 Å | ||||||
Authors | Sugrue, E. / Carr, P.D. / Khurana, J.L. / Jackson, C.J. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2015 Title: Evolutionary Expansion of the Amidohydrolase Superfamily in Bacteria in Response to the Synthetic Compounds Molinate and Diuron. Authors: Sugrue, E. / Fraser, N.J. / Hopkins, D.H. / Carr, P.D. / Khurana, J.L. / Oakeshott, J.G. / Scott, C. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4whb.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4whb.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4whb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whb ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whb | HTTPS FTP |
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-Related structure data
Related structure data | 4wgxSC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49748.871 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium brisbanense (bacteria) / Gene: puhB / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: B8R4K0 #2: Chemical | ChemComp-ZN / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.02% (v/v) sodium azide, 0.2 M MgCl, 8% (v/v) PEG MME 550, 8% w/v PEG 20000, 0.05 MES at ph 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.958→40.12 Å / Num. all: 75147 / Num. obs: 75147 / % possible obs: 99.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.201 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.96→3.02 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WGX Resolution: 2.958→39.595 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 235.4 Å2 / Biso mean: 41.0211 Å2 / Biso min: 0 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.958→39.595 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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