+Open data
-Basic information
Entry | Database: PDB / ID: 2pd6 | ||||||
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Title | Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8 | ||||||
Components | Estradiol 17-beta-dehydrogenase 8 | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase/reductase / steroid metabolism / lipid metabolism / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / estrogen biosynthetic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / Fatty acyl-CoA biosynthesis / testosterone dehydrogenase (NAD+) activity / NADH binding / oxidoreductase complex / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity ...(3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / estrogen biosynthetic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / Fatty acyl-CoA biosynthesis / testosterone dehydrogenase (NAD+) activity / NADH binding / oxidoreductase complex / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / mitochondrial envelope / protein heterotetramerization / androgen metabolic process / fatty acid biosynthetic process / mitochondrial matrix / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. ...Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8 Authors: Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. ...Authors: Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pd6.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pd6.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/2pd6 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/2pd6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27466.223 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B8, FABGL, HKE6, RING2 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 References: UniProt: Q92506, 17beta-estradiol 17-dehydrogenase #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
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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: 1.98 Å3/Da / Density % sol: 37.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM sodium fluoride, 20% PEG3350, 10% ethylene glycol plus 5mM NAD+, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00234 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2007 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00234 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 54998 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.117 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.759 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Swissmodel based on pdb entries 1Q7B and 1EDO Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.266 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.061 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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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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