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- PDB-2hdj: Crystal structure of human type 3 3alpha-hydroxysteroid dehydroge... -

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Basic information

Entry
Database: PDB / ID: 2hdj
TitleCrystal structure of human type 3 3alpha-hydroxysteroid dehydrogenase in complex with NADP(H)
ComponentsAldo-keto reductase family 1 member C2
KeywordsOXIDOREDUCTASE / HUMAN 3ALPHAHDS3 / ALDO-KETO REDUCTASE / NADPH / AKR / AKR1C2
Function / homology
Function and homology information


indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity ...indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / androsterone dehydrogenase activity / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / 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
Chem-NDP / Aldo-keto reductase family 1 member C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 20, 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 C2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,82014
Polymers73,5732
Non-polymers2,24812
Water9,872548
1
A: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8146
Polymers36,7861
Non-polymers1,0285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0068
Polymers36,7861
Non-polymers1,2207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Aldo-keto reductase family 1 member C2
hetero molecules

B: Aldo-keto reductase family 1 member C2
hetero molecules

B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,01824
Polymers110,3593
Non-polymers3,65921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9850 Å2
ΔGint-71 kcal/mol
Surface area38450 Å2
MethodPISA
4
A: Aldo-keto reductase family 1 member C2
hetero molecules

A: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,62812
Polymers73,5732
Non-polymers2,05510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_556x-y+1/3,-y+2/3,-z+5/31
Buried area5500 Å2
ΔGint-36 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.840, 143.840, 204.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-648-

HOH

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Components

#1: Protein Aldo-keto reductase family 1 member C2 / Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / Type III 3- alpha-hydroxysteroid ...Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / Type III 3- alpha-hydroxysteroid dehydrogenase / 3-alpha-HSD3 / Chlordecone reductase homolog HAKRD / Dihydrodiol dehydrogenase/bile acid-binding protein / DD/BABP / Dihydrodiol dehydrogenase 2 / DD2


Mass: 36786.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C2, DDH2 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS
References: UniProt: P52895, Oxidoreductases, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, EC: 1.1.1.213
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 24% PEG-4000, 0.1M MES, 0.2M (NH4)2Ac, 0.01M EDTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.19 Å / Num. all: 54795 / Num. obs: 54795 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.254 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.89
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2-2.10.4214.338164729598.6
2.1-2.20.3245.632649605299
2.2-2.30.2537.127854505498.9
2.3-2.40.2138.524052428399
2.4-2.50.1781020340361099.2
2.5-2.60.15211.417457307299.3
2.6-2.80.11714.528176494199.4
2.8-30.08518.921319372599.5
3-3.50.05526.934563601799.8
3.5-40.03935.919685341399.8
4-50.03144.319547339099.9
5-60.03468753151899.9
60.02155.69444166599.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1XJB

1xjb


Resolution: 2→19.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 9579143 / 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
Rfree0.226 2778 5.1 %RANDOM
Rwork0.196 ---
obs0.196 54442 99.8 %-
all-54795 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.447 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å23.75 Å20 Å2
2--2.72 Å20 Å2
3----5.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 140 548 5932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.422.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 447 4.9 %
Rwork0.268 8589 -
obs-9036 99.8 %
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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