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- PDB-2fgb: Crystal structure of human 17bet a-hydroxysteroid dehydrogenase t... -

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Basic information

Entry
Database: PDB / ID: 2fgb
TitleCrystal structure of human 17bet a-hydroxysteroid dehydrogenase type 5 in complexes with PEG and NADP
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE / (alpha/beta)8 barrel
Function / homology
Function and homology information


prostaglandin D2 11-ketoreductase activity / cellular response to corticosteroid stimulus / regulation of testosterone biosynthetic process / prostaglandin-F synthase / prostaglandin-F synthase activity / testosterone 17beta-dehydrogenase (NADP+) / cellular response to prostaglandin stimulus / negative regulation of retinoic acid biosynthetic process / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / ketoreductase activity ...prostaglandin D2 11-ketoreductase activity / cellular response to corticosteroid stimulus / regulation of testosterone biosynthetic process / prostaglandin-F synthase / prostaglandin-F synthase activity / testosterone 17beta-dehydrogenase (NADP+) / cellular response to prostaglandin stimulus / negative regulation of retinoic acid biosynthetic process / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / ketoreductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / cellular response to prostaglandin D stimulus / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / farnesol catabolic process / macromolecule metabolic process / cellular response to jasmonic acid stimulus / 3alpha-hydroxysteroid 3-dehydrogenase / delta4-3-oxosteroid 5beta-reductase activity / geranylgeranyl reductase activity / phenanthrene 9,10-monooxygenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / androsterone dehydrogenase activity / RA biosynthesis pathway / testosterone biosynthetic process / retinal metabolic process / regulation of retinoic acid receptor signaling pathway / dihydrotestosterone 17-beta-dehydrogenase activity / ketosteroid monooxygenase activity / steroid dehydrogenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / aldo-keto reductase (NADP) activity / NAD-retinol dehydrogenase activity / cyclooxygenase pathway / positive regulation of endothelial cell apoptotic process / prostaglandin H2 endoperoxidase reductase activity / NADP-retinol dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / bile acid binding / prostaglandin metabolic process / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / renal absorption / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / keratinocyte differentiation / cellular response to calcium ion / cellular response to starvation / response to nutrient / positive regulation of cell death / cellular response to cadmium ion / cellular response to reactive oxygen species / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of protein kinase B signaling / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsQiu, W. / Zhou, M. / Azzi, A. / Luu-The, V. / Labrie, F. / Lin, S.X.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure-based inhibitor design for an enzyme that binds different steroids: a potent inhibitor for human type 5 17beta-hydroxysteroid dehydrogenase.
Authors: Qiu, W. / Zhou, M. / Mazumdar, M. / Azzi, A. / Ghanmi, D. / Luu-The, V. / Labrie, F. / Lin, S.X.
History
DepositionDec 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9814
Polymers36,8961
Non-polymers1,0853
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.519, 61.653, 95.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldo-keto reductase family 1 member C3 / Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / 3-alpha- hydroxysteroid dehydrogenase type 2 ...Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / 3-alpha- hydroxysteroid dehydrogenase type 2 / 3-alpha-HSD type 2 / 3-alpha-HSD type II / brain / Prostaglandin F synthase / PGFS / Estradiol 17-beta-dehydrogenase / 17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / Chlordecone reductase homolog HAKRb / HA1753 / Dihydrodiol dehydrogenase type I / Dihydrodiol dehydrogenase 3 / DD3 / DD-3


Mass: 36896.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, KIAA0119, PGFS / Plasmid: PCMV-NEO / Production host: Escherichia coli (E. coli)
References: UniProt: P42330, 17beta-estradiol 17-dehydrogenase, EC: 1.1.1.213, prostaglandin-F synthase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1 M sodium citrate, 0.24 M ammonia sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→47.57 Å / Num. obs: 68644

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→47.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.773 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3468 5.1 %RANDOM
Rwork0.172 ---
all0.173 ---
obs-68644 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.651 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.35→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 71 394 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222761
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9973765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65823.937127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00615490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.761519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022093
X-RAY DIFFRACTIONr_nbd_refined0.1950.21403
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2337
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.257
X-RAY DIFFRACTIONr_mcbond_it0.6051.51676
X-RAY DIFFRACTIONr_mcangle_it0.94122666
X-RAY DIFFRACTIONr_scbond_it1.32631216
X-RAY DIFFRACTIONr_scangle_it1.9864.51083
LS refinement shellResolution: 1.35→1.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 149 -
Rwork0.259 3325 -
obs-3474 65.2 %

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