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Yorodumi- PDB-7kaz: Crystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kaz | |||||||||
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Title | Crystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staphylococcus aureus | |||||||||
Components | Oleate hydratase | |||||||||
Keywords | OXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / 18:1 / complex / oleic acid / hydroxystearic acid / FAD / h18:0 | |||||||||
Function / homology | Function and homology information oleate hydratase / oleate hydratase activity / FAD binding / fatty acid metabolic process Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å | |||||||||
Authors | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kaz.cif.gz | 731.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kaz.ent.gz | 598.7 KB | Display | PDB format |
PDBx/mmJSON format | 7kaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kaz_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7kaz_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7kaz_validation.xml.gz | 92.9 KB | Display | |
Data in CIF | 7kaz_validation.cif.gz | 144.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/7kaz ftp://data.pdbj.org/pub/pdb/validation_reports/ka/7kaz | HTTPS FTP |
-Related structure data
Related structure data | 7kavSC 7kawC 7kaxC 7kayC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules CBA
#1: Protein | Mass: 69834.688 Da / Num. of mol.: 3 / Mutation: E82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) 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: Escherichia coli (E. coli) / References: UniProt: A0A0D6GJV1 |
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-Non-polymers , 5 types, 2731 molecules
#2: Chemical | ChemComp-WAD / ( | ||||||
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#3: Chemical | #4: Chemical | ChemComp-K / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and ...Details: Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and 750 uM FAD. Cryo: 15% v/v PEG3000, 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019 |
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: 1.85→22.42 Å / Num. obs: 183821 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.04 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.8 % / Num. unique obs: 18078 / Rpim(I) all: 0.485 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KAV Resolution: 1.854→22.42 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.77 / 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: 112.29 Å2 / Biso mean: 29.2785 Å2 / Biso min: 6.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.854→22.42 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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