[English] 日本語
Yorodumi- PDB-7kaw: Crystal structure of OhyA-PEG400-FAD complex from Staphylococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kaw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of OhyA-PEG400-FAD complex from Staphylococcus aureus | |||||||||
Components | Oleate hydratase | |||||||||
Keywords | OXIDOREDUCTASE / Oleate hydratase / OhyA / SaOhyA / Complex / PEG400 / FAD | |||||||||
Function / homology | oleate hydratase / oleate hydratase activity / Oleate hydratase / MCRA family / FAD binding / fatty acid metabolic process / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Myosin-cross-reactive antigen Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å | |||||||||
Authors | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | United States, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7kaw.cif.gz | 407.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7kaw.ent.gz | 324.8 KB | Display | PDB format |
PDBx/mmJSON format | 7kaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kaw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7kaw_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7kaw_validation.xml.gz | 83 KB | Display | |
Data in CIF | 7kaw_validation.cif.gz | 122.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/7kaw ftp://data.pdbj.org/pub/pdb/validation_reports/ka/7kaw | HTTPS FTP |
-Related structure data
Related structure data | 7kavSC 7kaxC 7kayC 7kazC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 69892.719 Da / Num. of mol.: 3 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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.22 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: Crystallized in: 20% PEG 400, 100 mM calcium acetate, 100 mM MES, pH 6.0; Soaked in same buffer containing 750 uM FAD. Cryo: 20% PEG 400, 100 mM calcium acetate, 100 mM MES, pH 6.0, 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 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: 2.1→23 Å / Num. obs: 126745 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rpim(I) all: 0.023 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12711 / Rpim(I) all: 0.135 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KAV Resolution: 2.105→22.999 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.46 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.07 Å2 / Biso mean: 35.8638 Å2 / Biso min: 15.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.105→22.999 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|