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Yorodumi- PDB-4xuk: Crystal structure of hydrolase AbOPH in beta lactamase superfamily -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xuk | ||||||
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Title | Crystal structure of hydrolase AbOPH in beta lactamase superfamily | ||||||
Components | Putative hydrolase | ||||||
Keywords | HYDROLASE / beta lactamase superfamily / organophosphate / phosphotriesterase / lactonase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter sp. NBRC 100985 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Chen, J. / Xu, J.H. / Zhou, J.H. | ||||||
Citation | Journal: Bioresour Bioprocess / Year: 2015 Title: Marked enhancement of Acinetobacter sp. organophosphorus hydrolase activity by a single residue substitution Ile211Ala Authors: Chen, J. / Lu, X.J. / Chen, Q. / Pan, J. / Zhou, J.H. / Xu, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xuk.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xuk.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xuk_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 4xuk_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 4xuk_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 4xuk_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xuk ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xuk | HTTPS FTP |
-Related structure data
Related structure data | 4le6S 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: 32284.404 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 48-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. NBRC 100985 (bacteria) Strain: NBRC 100985 / Gene: ACT4_021_01090 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G7GD18 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | gene mutations in the process of PCR | |
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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: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.12 M Monosaccharides(0.2 M D-glucose, 0.2 M D-mannose,0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M Buffer system 1(1M MES/Imidazole), pH 6.5, 12. ...Details: 0.12 M Monosaccharides(0.2 M D-glucose, 0.2 M D-mannose,0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M Buffer system 1(1M MES/Imidazole), pH 6.5, 12.5% (w/v) PEG1000, 12.5% (w/v) PEG3350, 12.5% (v/v) MPD PH range: 5.7-6.9 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 17, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 43098 / % possible obs: 98.6 % / Redundancy: 12 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Χ2: 1.031 / Net I/av σ(I): 31.312 / Net I/σ(I): 28.3 / Num. measured all: 515255 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LE6 Resolution: 2→34.836 Å / FOM work R set: 0.8332 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.33 / 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: 65.93 Å2 / Biso mean: 23.65 Å2 / Biso min: 12.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→34.836 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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