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- PDB-2ag5: Crystal Structure of Human DHRS6 -

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Basic information

Entry
Database: PDB / ID: 2ag5
TitleCrystal Structure of Human DHRS6
Componentsdehydrogenase/reductase (SDR family) member 6
KeywordsOXIDOREDUCTASE / 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
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyrate dehydrogenase type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKunde, G. / Lukacik, P. / Papagrigoriou, E. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: 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
DepositionJul 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2012Group: Database references
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dehydrogenase/reductase (SDR family) member 6
B: dehydrogenase/reductase (SDR family) member 6
C: dehydrogenase/reductase (SDR family) member 6
D: dehydrogenase/reductase (SDR family) member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,28112
Polymers107,2434
Non-polymers3,0388
Water15,637868
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18250 Å2
ΔGint-193 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.092, 62.055, 74.042
Angle α, β, γ (deg.)106.05, 105.95, 100.97
Int Tables number1
Space group name H-MP1
DetailsTHE 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

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Components

#1: Protein
dehydrogenase/reductase (SDR family) member 6 / DHRS6


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 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→66.67 Å / Num. all: 84879 / Num. obs: 76176 / % possible obs: 89.7 %
Reflection shellResolution: 1.84→1.9 Å / % possible all: 52.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.22417 1464 1.9 %RANDOM
Rwork0.16691 ---
all0.16797 ---
obs0.16797 74714 89.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0.09 Å20.27 Å2
2---0.36 Å20.32 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.84→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7365 0 196 868 8429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227771
X-RAY DIFFRACTIONr_bond_other_d0.0020.027091
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.98510569
X-RAY DIFFRACTIONr_angle_other_deg0.925316460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36424.908326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25151312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1681547
X-RAY DIFFRACTIONr_chiral_restr0.1060.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021471
X-RAY DIFFRACTIONr_nbd_refined0.2130.21699
X-RAY DIFFRACTIONr_nbd_other0.1930.27420
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23883
X-RAY DIFFRACTIONr_nbtor_other0.0880.24224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0181.55078
X-RAY DIFFRACTIONr_mcbond_other0.3261.52032
X-RAY DIFFRACTIONr_mcangle_it1.42227860
X-RAY DIFFRACTIONr_scbond_it2.50433133
X-RAY DIFFRACTIONr_scangle_it3.5054.52703
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 46 -
Rwork0.204 3250 -
obs--52.25 %

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