+Open data
-Basic information
Entry | Database: PDB / ID: 6oht | ||||||
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Title | Structure of EBP and U18666A | ||||||
Components | 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase | ||||||
Keywords | Membrane protein / isomerase/inhibitor / Isomerase / isomerase-inhibitor complex | ||||||
Function / homology | Function and homology information cholestenol Delta-isomerase / C-8 sterol isomerase activity / cholesterol biosynthetic process via desmosterol / cholesterol biosynthetic process via lathosterol / cholestenol delta-isomerase activity / Cholesterol biosynthesis via desmosterol / Cholesterol biosynthesis via lathosterol / steroid delta-isomerase activity / ossification involved in bone maturation / cholesterol biosynthetic process ...cholestenol Delta-isomerase / C-8 sterol isomerase activity / cholesterol biosynthetic process via desmosterol / cholesterol biosynthetic process via lathosterol / cholestenol delta-isomerase activity / Cholesterol biosynthesis via desmosterol / Cholesterol biosynthesis via lathosterol / steroid delta-isomerase activity / ossification involved in bone maturation / cholesterol biosynthetic process / hemopoiesis / cholesterol metabolic process / nuclear envelope / cytoplasmic vesicle / nuclear membrane / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Long, T. / Li, X. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for human sterol isomerase in cholesterol biosynthesis and multidrug recognition. Authors: Long, T. / Hassan, A. / Thompson, B.M. / McDonald, J.G. / Wang, J. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oht.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oht.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 6oht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oht_validation.pdf.gz | 984.3 KB | Display | wwPDB validaton report |
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Full document | 6oht_full_validation.pdf.gz | 1009.9 KB | Display | |
Data in XML | 6oht_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 6oht_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/6oht ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6oht | HTTPS FTP |
-Related 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
#1: Protein | Mass: 27562.555 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EBP / Production host: Homo sapiens (human) / References: UniProt: Q15125, cholestenol Delta-isomerase #2: Chemical | |
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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: 3.88 Å3/Da / Density % sol: 68.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Hepes, peg 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 28389 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.99 / Net I/σ(I): 30 |
Reflection shell | Resolution: 3.1382→3.26 Å / Num. unique obs: 2273 / CC1/2: 0.739 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→48.642 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→48.642 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -26.5989 Å / Origin y: -4.861 Å / Origin z: 43.3307 Å
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Refinement TLS group | Selection details: all |