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Yorodumi- PDB-2o23: The structure of wild-type human HADH2 (17beta-hydroxysteroid deh... -
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-Basic information
Entry | Database: PDB / ID: 2o23 | ||||||
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Title | The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A | ||||||
Components | HADH2 protein | ||||||
Keywords | OXIDOREDUCTASE / HSD17B10 / SCHAD / ERAB / Type II HADH / 2-Methyl-3-hydroxybutyryl-CoA dehydrogenase / MHBD / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex ...mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / 3(or 17)beta-hydroxysteroid dehydrogenase / testosterone dehydrogenase [NAD(P)] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3-hydroxyacyl-CoA dehydrogenase activity / branched-chain amino acid catabolic process / bile acid biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Kavanagh, K.L. / Shafqat, N. / Scholer, K. / Debreczeni, J. / Zschocke, J. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. ...Kavanagh, K.L. / Shafqat, N. / Scholer, K. / Debreczeni, J. / Zschocke, J. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A Authors: KAVANAGH, K.L. / SHAFQAT, N. / SCHOLER, K. / DEBRECZENI, J. / ZSCHOCKE, J. / von Delft, F. / WEIGELT, J. / ARROWSMITH, C. / SUNDSTROM, M. / EDWARDS, A. / OPPERMANN, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o23.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o23.ent.gz | 182.6 KB | Display | PDB format |
PDBx/mmJSON format | 2o23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o23 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o23 | HTTPS FTP |
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-Related structure data
Related structure data | 1u7tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27286.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HADH2 / Plasmid: pET11-derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6IBS9, UniProt: Q99714*PLUS, 3-hydroxy-2-methylbutyryl-CoA dehydrogenase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25.5% PEG 3350, 15% glycerol, 0.17 M ammonium sulfate, 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: 0.9687 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9687 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 168585 / Num. obs: 168585 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 24386 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1U7T Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.028 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.03 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.171 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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