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- PDB-1j96: Human 3alpha-HSD type 3 in Ternary Complex with NADP and Testosterone -

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Basic information

Entry
Database: PDB / ID: 1j96
TitleHuman 3alpha-HSD type 3 in Ternary Complex with NADP and Testosterone
Components3alpha-hydroxysteroid dehydrogenase type 3
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / steroid metabolism
Function / homology
Function and homology information


indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase [NAD(P)+] activity / cellular response to prostaglandin D stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase ...indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase [NAD(P)+] activity / cellular response to prostaglandin D stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / ketosteroid monooxygenase activity / progesterone metabolic process / carboxylic acid binding / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Oxidoreductases / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / aldose reductase (NADPH) activity / prostaglandin metabolic process / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / epithelial cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / 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 / TESTOSTERONE / Aldo-keto reductase family 1 member C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNahoum, V. / Labrie, F. / Lin, S.-X.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure of the human 3alpha-hydroxysteroid dehydrogenase type 3 in complex with testosterone and NADP at 1.25-A resolution.
Authors: Nahoum, V. / Gangloff, A. / Legrand, P. / Zhu, D.W. / Cantin, L. / Zhorov, B.S. / Luu-The, V. / Labrie, F. / Breton, R. / Lin, S.X.
History
DepositionMay 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: 3alpha-hydroxysteroid dehydrogenase type 3
B: 3alpha-hydroxysteroid dehydrogenase type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7228
Polymers73,5402
Non-polymers2,1826
Water15,457858
1
A: 3alpha-hydroxysteroid dehydrogenase type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8614
Polymers36,7701
Non-polymers1,0913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3alpha-hydroxysteroid dehydrogenase type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8614
Polymers36,7701
Non-polymers1,0913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.072, 87.148, 76.877
Angle α, β, γ (deg.)90.00, 107.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3alpha-hydroxysteroid dehydrogenase type 3 / 3alpha-hydroxycholanate dehydrogenase


Mass: 36770.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P52895, EC: 1.1.1.213
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, ammonium acetate, MPD, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.26 Mammonium acetate1reservoir
327 %(w/v)PEG40001reservoir
42.5 %MPD1reservoir
50.06 %beta-octylglucoside1reservoir
60.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9511 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 13, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9511 Å / Relative weight: 1
ReflectionResolution: 1.25→10 Å / Num. all: 180714 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.78 % / Biso Wilson estimate: 12.38 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.3
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 1.97 / Num. unique all: 17523 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 180714 / Redundancy: 3.8 % / Num. measured all: 682343 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 93.9 % / Redundancy: 6.7 % / Num. unique obs: 17523 / Num. measured obs: 118043 / Rmerge(I) obs: 0.172

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Processing

Software
NameClassification
EPMRphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFS

1afs


Resolution: 1.25→10 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.199 8672 RANDOM
Rwork0.181 --
all-180677 -
obs-180677 -
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 146 858 6146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.8
X-RAY DIFFRACTIONp_bond_d0.008
LS refinement shellResolution: 1.25→1.307 Å
RfactorNum. reflection
Rfree0.23 1066
Rwork0.219 -
obs-20235
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.181 / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.219 / Rfactor obs: 0.219

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