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- PDB-2he5: Crystal structure of 17alpha-hydroxysteroid dehydrogenase in bina... -

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Basic information

Entry
Database: PDB / ID: 2he5
TitleCrystal structure of 17alpha-hydroxysteroid dehydrogenase in binary complex with NADP(H) in an open conformation
ComponentsAldo-keto reductase family 1, member C21
KeywordsOXIDOREDUCTASE / 17a-HSD / AKR1C21 / AKR / aldo-keto reductase / HSD / hydroxysteroid dehydrogenase / open conformation
Function / homology
Function and homology information


17-beta-ketosteroid reductase activity / chlordecone reductase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / phenanthrene 9,10-monooxygenase activity ...17-beta-ketosteroid reductase activity / chlordecone reductase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / carboxylic acid binding / aldo-keto reductase (NADPH) activity / lithocholic acid binding / steroid biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / retinal dehydrogenase activity / bile acid binding / aldose reductase (NADPH) activity / NADP+ binding / steroid metabolic process / NADPH binding / steroid binding / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / 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 / BETA-MERCAPTOETHANOL / Chem-NDP / Aldo-keto reductase family 1 member C21 / Aldo-keto reductase family 1 member C21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFaucher, F. / Pereira de Jesus-Tran, K. / Cantin, L. / Luu-the, V. / Labrie, F. / Breton, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Mouse 17alpha-Hydroxysteroid Dehydrogenase (Apoenzyme and Enzyme-NADP(H) Binary Complex): Identification of Molecular Determinants Responsible for the Unique 17alpha- ...Title: Crystal Structures of Mouse 17alpha-Hydroxysteroid Dehydrogenase (Apoenzyme and Enzyme-NADP(H) Binary Complex): Identification of Molecular Determinants Responsible for the Unique 17alpha-reductive Activity of this Enzyme.
Authors: Faucher, F. / Pereira de Jesus-Tran, K. / Cantin, L. / Luu-The, V. / Labrie, F. / Breton, R.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aldo-keto reductase family 1, member C21
B: Aldo-keto reductase family 1, member C21
C: Aldo-keto reductase family 1, member C21
D: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,87611
Polymers147,6984
Non-polymers3,1787
Water2,468137
1
A: Aldo-keto reductase family 1, member C21
C: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4776
Polymers73,8492
Non-polymers1,6284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-30 kcal/mol
Surface area25760 Å2
MethodPISA
2
B: Aldo-keto reductase family 1, member C21
D: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3995
Polymers73,8492
Non-polymers1,5503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-27 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.480, 166.760, 69.550
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldo-keto reductase family 1, member C21


Mass: 36924.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c21 / Plasmid: pGEX1lT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: Q9CX32, UniProt: Q91WR5*PLUS
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 44.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 22-24% PEG-4000, 0.1M MES, 0.2M (NH4)2Ac, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.933 Å
DetectorDetector: CCD / Date: Dec 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→19.91 Å / Num. all: 27939 / Num. obs: 27939 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.582 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.01
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.9-30.3683.48479264097.7
3-3.20.2994.114199440798.6
3.2-3.50.202615934492199.5
3.5-40.1418.317043525799.2
4-50.08712.416787516298.4
5-60.07213.97557231299.2
60.053177983248198.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2302222.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1403 5 %RANDOM
Rwork0.218 ---
obs0.218 27717 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.435 Å2 / ksol: 0.256 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.84 Å20 Å2-0.96 Å2
2--6.31 Å20 Å2
3----11.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10148 0 200 141 10489
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.272
X-RAY DIFFRACTIONc_scangle_it22.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 244 5.3 %
Rwork0.323 4389 -
obs-4633 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligands_.paramligands_.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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