+Open data
-Basic information
Entry | Database: PDB / ID: 8g84 | ||||||
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Title | Crystal structures of HSD17B13 complexes | ||||||
Components | Hydroxysteroid 17-beta dehydrogenase 13 | ||||||
Keywords | OXIDOREDUCTASE / 17 beta-hydroxysteroid dehydrogenase 13 / lipid droplet associated protein / inhibitor | ||||||
Function / homology | short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Hydroxysteroid 17-beta dehydrogenase 13 Function and homology information | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.467 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 | 8g84.cif.gz | 246.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g84.ent.gz | 199.8 KB | Display | PDB format |
PDBx/mmJSON format | 8g84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/8g84 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/8g84 | HTTPS FTP |
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-Related structure data
Related structure data | 8g89C 8g93C 8g9vC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35364.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSD17B13 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8C0PP93 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 3.52 Å3/Da / Density % sol: 65.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG3350, 0.2 M ammonium chloride |
-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: Oct 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.467→93.6 Å / Num. obs: 29109 / % possible obs: 93.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rpim(I) all: 0.077 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.467→2.64 Å / Redundancy: 6.8 % / Num. unique obs: 1456 / CC1/2: 0.581 / Rpim(I) all: 0.579 / % possible all: 50.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.467→24.16 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.375 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.379 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.244
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Displacement parameters | Biso mean: 56.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.467→24.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.47→2.58 Å
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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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