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- PDB-2hej: Crystal structure of 17alpha-hydroxysteroid dehydrogenase in comp... -

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Basic information

Entry
Database: PDB / ID: 2hej
TitleCrystal structure of 17alpha-hydroxysteroid dehydrogenase in complex with NADP(H) in a closed conformation
ComponentsAldo-keto reductase family 1, member C21
KeywordsOXIDOREDUCTASE / 17a-HSD / AKR1C21 / AKR / aldo-keto reductase / HSD / hydroxysteroid dehydrogenase / closed 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
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: 1.35 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 1.3Aug 30, 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,04313
Polymers73,8492
Non-polymers2,19411
Water13,619756
1
A: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1158
Polymers36,9251
Non-polymers1,1907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9285
Polymers36,9251
Non-polymers1,0044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.500, 53.600, 86.500
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36924.578 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 767 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 18% PEG-6000, 0.1M HEPES, 5% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→38.13 Å / Num. all: 142410 / Num. obs: 142410 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.891 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.88
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.35-1.40.2634.3379921348687.9
1.4-1.60.1666.61154044049992.1
1.6-1.80.07912.7749842572196.5
1.8-20.06615464111610694.5
2-2.50.05822937862134595.1
2.5-30.04930.156873950695.2
3-40.04141.641065741493.3
4-50.0350.513199263591.4
5-100.03445.712639237688.7
100.02446.2121031678.2

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Phasing

Phasing MRRfactor: 0.362 / Cor.coef. Fo:Fc: 0.647
Highest resolutionLowest resolution
Rotation3 Å45.52 Å
Translation3 Å45.52 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2HE8

2he8


Resolution: 1.35→38.13 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.855 / Data cutoff high absF: 1548498.5 / 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
Rfree0.218 7147 5 %RANDOM
Rwork0.201 ---
all0.201 142410 --
obs0.201 139404 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.545 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0.56 Å2
2--0.89 Å20 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.35→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5195 0 116 780 6091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.282.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.35-1.360.321310.28927522883
1.36-1.370.4041420.37624952637
1.37-1.380.4121240.38824482572
1.38-1.390.2881530.27827692922
1.39-1.40.2671580.24827242882
1.4-1.410.2931470.24827622909
1.41-1.420.251470.24527672914
1.42-1.430.2891480.24827552903
1.43-1.440.3211400.28526372777
1.44-1.450.2991550.29126602815
1.45-1.470.2451400.23927462886
1.47-1.480.3221250.31325022627
1.48-1.490.2291440.23127722916
1.49-1.510.2511600.22527082868
1.51-1.520.2871170.28926212738
1.52-1.540.341400.32324162556
1.54-1.550.2411510.2227842935
1.55-1.570.2391380.21627312869
1.57-1.580.2671400.21428012941
1.58-1.60.2021370.20727642901
1.6-1.620.2411560.20127802936
1.62-1.640.1981560.227712927
1.64-1.660.2121430.19627702913
1.66-1.680.211500.19527812931
1.68-1.70.2091490.19728172966
1.7-1.720.2051540.1926502804
1.72-1.750.2351400.19927302870
1.75-1.770.2251320.19428412973
1.77-1.80.221540.19627722926
1.8-1.830.2151510.19627732924
1.83-1.860.1971370.18627862923
1.86-1.90.2281260.20226862812
1.9-1.930.2741340.28225532687
1.93-1.970.2151420.19727372879
1.97-2.020.2091410.18427552896
2.02-2.060.2141540.20326752829
2.06-2.120.2961350.24625702705
2.12-2.170.1991600.18527452905
2.17-2.240.1871470.18727562903
2.24-2.310.2271300.20626882818
2.31-2.390.1991420.1927452887
2.39-2.490.2171380.18127822920
2.49-2.60.2231570.19127182875
2.6-2.740.2021270.18627122839
2.74-2.910.2021680.18627142882
2.91-3.130.1991540.18227032857
3.13-3.450.1711270.16426812808
3.45-3.950.181200.15527082828
3.95-4.970.1331590.13726222781
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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