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- PDB-7f30: Crystal structure of OxdB E85A in complex with Z-2- (3-bromopheny... -
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Open data
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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 | ||||||
![]() | Phenylacetaldoxime dehydratase | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muraki, N. / Matsui, D. / Asano, Y. / Aono, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 61.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7f2yC ![]() 7f2zC ![]() 3a15S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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