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- PDB-7kay: Crystal structure of OhyA(E82A)-18:1 complex from Staphylococcus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kay | |||||||||
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Title | Crystal structure of OhyA(E82A)-18:1 complex from Staphylococcus aureus | |||||||||
![]() | Oleate hydratase | |||||||||
![]() | OXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / 18:1 / complex / oleic acid | |||||||||
Function / homology | ![]() oleate hydratase / oleate hydratase activity / FAD binding / fatty acid metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and mechanism of Staphylococcus aureus oleate hydratase (OhyA). Authors: Radka, C.D. / Batte, J.L. / Frank, M.W. / Young, B.M. / Rock, C.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413.7 KB | Display | ![]() |
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PDB format | ![]() | 330.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1004.3 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 86.1 KB | Display | |
Data in CIF | ![]() | 131.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kavSC ![]() 7kawC ![]() 7kaxC ![]() 7kazC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 69834.688 Da / Num. of mol.: 3 / Mutation: E82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_ ...Gene: DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_02399, NCTC10654_00136, RK64_00980 Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystallized: 15% PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5. Cryo: 15% PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, 30% glycerol |
-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: Feb 6, 2020 |
Radiation | Monochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→29.459 Å / Num. obs: 150514 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rpim(I) all: 0.041 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.1 % / Num. unique obs: 10700 / Rpim(I) all: 0.399 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7KAV Resolution: 1.95→22.46 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.45 / 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: 84.91 Å2 / Biso mean: 24.8419 Å2 / Biso min: 7.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→22.46 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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