+Open data
-Basic information
Entry | Database: PDB / ID: 8g9v | ||||||
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Title | Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13 | ||||||
Components | 17-beta-hydroxysteroid dehydrogenase 13 | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / 17 beta-hydroxysteroid dehydrogenase 13 / lipid droplet associated protein / inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information Lipid particle organization / all-trans-retinol dehydrogenase (NAD+) / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid dehydrogenase activity / 17beta-estradiol 17-dehydrogenase / all-trans-retinol dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / positive regulation of lipid biosynthetic process / lipid droplet ...Lipid particle organization / all-trans-retinol dehydrogenase (NAD+) / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid dehydrogenase activity / 17beta-estradiol 17-dehydrogenase / all-trans-retinol dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / positive regulation of lipid biosynthetic process / lipid droplet / lipid metabolic process / endoplasmic reticulum / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 Å | ||||||
Authors | Liu, S. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of lipid-droplet localization of 17-beta-hydroxysteroid dehydrogenase 13. Authors: Liu, S. / Sommese, R.F. / Nedoma, N.L. / Stevens, L.M. / Dutra, J.K. / Zhang, L. / Edmonds, D.J. / Wang, Y. / Garnsey, M. / Clasquin, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g9v.cif.gz | 890.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g9v.ent.gz | 746.7 KB | Display | PDB format |
PDBx/mmJSON format | 8g9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g9v_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 8g9v_full_validation.pdf.gz | 5 MB | Display | |
Data in XML | 8g9v_validation.xml.gz | 81.5 KB | Display | |
Data in CIF | 8g9v_validation.cif.gz | 105.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/8g9v ftp://data.pdbj.org/pub/pdb/validation_reports/g9/8g9v | HTTPS FTP |
-Related structure data
Related structure data | 8g84C 8g89C 8g93C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 35502.348 Da / Num. of mol.: 8 / Mutation: Q60K, I62R, R71H, E161K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B13, SCDR9, SDR16C3, HMFN0376, UNQ497/PRO1014 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q7Z5P4, Oxidoreductases; Acting on the CH-OH group of donors |
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-Non-polymers , 5 types, 60 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-YYC / #4: Chemical | ChemComp-CE1 / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-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: 2.75 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.645→90.95 Å / Num. obs: 67940 / % possible obs: 93.4 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rpim(I) all: 0.083 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.645→2.897 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3398 / CC1/2: 0.462 / Rpim(I) all: 0.589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.645→37.91 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
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Displacement parameters | Biso mean: 61.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.645→37.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.8 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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