+Open data
-Basic information
Entry | Database: PDB / ID: 2ag5 | ||||||
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Title | Crystal Structure of Human DHRS6 | ||||||
Components | dehydrogenase/reductase (SDR family) member 6 | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN-co-FACTOR complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ketone body biosynthetic process / Synthesis of Ketone Bodies / 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / heme metabolic process / : / siderophore biosynthetic process / 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 ...ketone body biosynthetic process / Synthesis of Ketone Bodies / 3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / heme metabolic process / : / siderophore biosynthetic process / 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 / fatty acid beta-oxidation / epithelial cell differentiation / NAD binding / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Kunde, G. / Lukacik, P. / Papagrigoriou, E. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Characterization of human DHRS6, an orphan short chain dehydrogenase/reductase enzyme: a novel, cytosolic type 2 R-beta-hydroxybutyrate dehydrogenase Authors: Guo, K. / Lukacik, P. / Papagrigoriou, E. / Meier, M. / Lee, W.H. / Adamski, J. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ag5.cif.gz | 215.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ag5.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 2ag5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2ag5 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2ag5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE BIOLOGICAL UNIT IS A HOMOTETRAMER. CHAIN A CAN GENERATE THE REST OF THE BIOLOGICAL UNIT IF THE FOLLOWING OPERATIONS ARE APPLIED: 90.04 -39.50 180.0 25.11 30.35 65.64, 89.95 50.48 180.0 65.72 -54.12 65.63, 0.071 -7.82 179.98 90.69 -23.77 -0.076 |
-Components
#1: Protein | Mass: 26810.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHRS6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUT1 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAD / #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: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ammonium sulphate, Mes, PEG monomethylether 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→66.67 Å / Num. all: 84879 / Num. obs: 76176 / % possible obs: 89.7 % |
Reflection shell | Resolution: 1.84→1.9 Å / % possible all: 52.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→66.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.647 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.145 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→66.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Total num. of bins used: 20
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