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- EMDB-42487: Cryo-EM reconstruction of Staphylococcus aureus oleate hydratase ... -
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Open data
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Basic information
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Title | Cryo-EM reconstruction of Staphylococcus aureus oleate hydratase (OhyA) dimer of dimers | |||||||||
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![]() | oleate hydratase (OhyA) / phospholipids / membrane binding domain / amphipathic helices / interfacial enzyme / peripheral membrane protein / HYDROLASE | |||||||||
Function / homology | oleate hydratase / oleate hydratase activity / Oleate hydratase / MCRA family / fatty acid metabolic process / FAD binding / FAD/NAD(P)-binding domain superfamily / Myosin-cross-reactive antigen![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
![]() | Oldham ML / Qayyum MZ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer Authors: Radka CD / Grace CR / Hasdemir HS / Li Y / Rodriguez CC / Rodrigues P / Oldham ML / Qayyum MZ / Pitre A / MacCain WJ / Kalathur RC / Tajkhorshid E / Rock CO | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 67.5 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 59.8 MB 62.2 MB 62.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ur8 M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.044 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: DeepEMhancer map
File | emd_42487_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42487_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42487_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dimer of Dimers of OhyA
Entire | Name: Dimer of Dimers of OhyA |
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Components |
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-Supramolecule #1: Dimer of Dimers of OhyA
Supramolecule | Name: Dimer of Dimers of OhyA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 278.686 KDa |
-Macromolecule #1: Oleate hydratase
Macromolecule | Name: Oleate hydratase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 69.892719 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MYYSYGNYEA FARPKKPENV ENKSAYLIGS GLASLAAACF LIRDGQMEGS KIHILEELPK AGGSLDGEN MPLKGYVVRG GREMENHFEC LWDLFRSIPS LEIDNASVLD EFYWLNKEDP NYSRCRVIEK QGQRLVTDGD F TLTKTAIK ...String: MGSSHHHHHH SSGLVPRGSH MYYSYGNYEA FARPKKPENV ENKSAYLIGS GLASLAAACF LIRDGQMEGS KIHILEELPK AGGSLDGEN MPLKGYVVRG GREMENHFEC LWDLFRSIPS LEIDNASVLD EFYWLNKEDP NYSRCRVIEK QGQRLVTDGD F TLTKTAIK EILDLCLTNE EDLDDVKITD VFSDDFFNSN FWIYWKTMFA FEPWHSAMEM RRYLMRFVHH ISGLADFSAL KF TKYNQYE SLVLPMVEYL KSHGVQFEYD VKVEDIKIDV TTSQKIAREI LIDRNGNAES IKLTINDLVF VTNGSITESS TYG DNDTPA PPTDELGGSW TLWKNLARQS PEFGNPDKFC QNIPKKSWFV SATSTTNNKE IIDTIESICK RDPLAGKTVT GGII TINDS AWQMSFTINR QQQFKDQPEN EISTWIYALY SDVNGDYIKK PITECSGNEI CQEWLYHLGV STDKIEDLAK HASNT IPVY MPYITSYFMT RAIGDRPLVV PHQSQNLAFI GNFAETERDT VFTTEYSVRT AMEAVYQLLN IDRGIPEVIN SPFDLR VLM DAIYELNDHQ DLREITKDSK MQKLALAGFL KKIKGTYIES LLKEHKLL UniProtKB: Myosin-cross-reactive antigen |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL | ||||||||||||
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Buffer | pH: 7.3 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Max: 100.0 K |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 276 / Average exposure time: 3.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 79000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: initial model was a crystal structure |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]()
PDB-8ur8: |