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Yorodumi- PDB-7f30: Crystal structure of OxdB E85A in complex with Z-2- (3-bromopheny... -
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-Basic information
Entry | Database: PDB / ID: 7f30 | ||||||
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Title | Crystal structure of OxdB E85A in complex with Z-2- (3-bromophenyl) propanal oxime | ||||||
Components | Phenylacetaldoxime dehydratase | ||||||
Keywords | LYASE / Aldoxime dehydratase / heme | ||||||
Function / homology | phenylacetaldoxime dehydratase / phenylacetaldoxime dehydratase activity / Haem-containing dehydratase / Haem-containing dehydratase / metal ion binding / Z-2-(3-bromophenyl) propanal oxime / PROTOPORPHYRIN IX CONTAINING FE / Phenylacetaldoxime dehydratase Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Muraki, N. / Matsui, D. / Asano, Y. / Aono, S. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2022 Title: Crystal structural analysis of aldoxime dehydratase from Bacillus sp. OxB-1: Importance of surface residues in optimization for crystallization. Authors: Matsui, D. / Muraki, N. / Chen, K. / Mori, T. / Ingram, A.A. / Oike, K. / Groger, H. / Aono, S. / Asano, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f30.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f30.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 7f30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f30_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7f30_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7f30_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7f30_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/7f30 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f30 | HTTPS FTP |
-Related structure data
Related structure data | 7f2yC 7f2zC 3a15S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41670.863 Da / Num. of mol.: 1 / Mutation: E85A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (strain OxB-1) (bacteria) / Strain: OxB-1 / Gene: oxd / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P82604, EC: 4.99.1.7 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-0WQ / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 39.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% (w/v) polyethylene glycol 4,000, 0.1 M Tris pH8.5, and 0.2 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.91939 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91939 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.792 Å / Num. obs: 22681 / % possible obs: 99.73 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05767 / Rpim(I) all: 0.03633 / Rrim(I) all: 0.06835 / Net I/σ(I): 14.41 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5143 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 2264 / CC1/2: 0.827 / Rpim(I) all: 0.3174 / Rrim(I) all: 0.6058 / % possible all: 99.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3a15 Resolution: 2→40.792 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.792 Å
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Refine LS restraints |
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LS refinement shell |
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