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- PDB-1mrq: Crystal structure of human 20alpha-HSD in ternary complex with NA... -

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Basic information

Entry
Database: PDB / ID: 1mrq
TitleCrystal structure of human 20alpha-HSD in ternary complex with NADP and 20alpha-hydroxy-progesterone
ComponentsAldo-keto reductase family 1 member C1
KeywordsOXIDOREDUCTASE / 20alpha-HSD / hydroxysteroid dehydrogenase / progesterone / ternary complex
Function / homology
Function and homology information


3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / androsterone dehydrogenase (B-specific) activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase ...3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / androsterone dehydrogenase (B-specific) activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / testosterone dehydrogenase [NAD(P)+] activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / dihydrotestosterone 17-beta-dehydrogenase activity / androsterone dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / response to organophosphorus / intestinal cholesterol absorption / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / retinal metabolic process / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / carboxylic acid binding / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / aldo-keto reductase (NADPH) activity / bile acid metabolic process / bile acid and bile salt transport / 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 / bile acid binding / aldose reductase (NADPH) activity / retinoid metabolic process / Prednisone ADME / prostaglandin 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 / digestion / epithelial cell differentiation / xenobiotic metabolic process / cholesterol homeostasis / positive regulation of reactive oxygen species metabolic process / extracellular exosome / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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 ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PROGESTERONE / Aldo-keto reductase family 1 member C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsCouture, J.F. / Legrand, P. / Cantin, L. / Luu-The, V. / Labrie, F. / Breton, R.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Human 20alpha-hydroxysteroid dehydrogenase: crystallographic and site-directed mutagenesis studies lead to the identification of an alternative binding site for C21-steroids.
Authors: Couture, J.F. / Legrand, P. / Cantin, L. / Luu-The, V. / Labrie, F. / Breton, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Expression, crystallization and preliminary X-ray analysis of human and rabbit 20alpha-hydroxysteroid dehydrogenase in complex with NADP(H) and various steroid substrates
Authors: Couture, J.F. / Cantin, L. / Legrand, P. / Luu-The, V. / Labrie, F. / Breton, R.
History
DepositionSep 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: 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

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9724
Polymers36,8361
Non-polymers1,1363
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.650, 83.540, 100.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a monomer

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Components

#1: Protein Aldo-keto reductase family 1 member C1 / 20alpha-hydroxysteroid dehydrogenase / Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / High- ...20alpha-hydroxysteroid dehydrogenase / Trans-1 / 2- dihydrobenzene-1 / 2-diol dehydrogenase / High-affinity hepatic bile acid-binding protein / HBAB / Chlordecone reductase homolog HAKRC / Dihydrodiol dehydrogenase 2 / DD2


Mass: 36836.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: liver / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q04828, 20alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, HEPES, ammonium sulfate, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
210 mM1reservoirK2HPO4
31 mMEDTA1reservoir
41 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 16, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 43980 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.8
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1482 / % possible all: 60.6
Reflection
*PLUS
Num. obs: 44183 / % possible obs: 95.9 % / Num. measured all: 295545
Reflection shell
*PLUS
% possible obs: 60.6 % / Num. unique obs: 1482 / Num. measured obs: 3622

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Processing

Software
NameVersionClassification
XDSdata reduction
AMoREphasing
REFMAC5.1.07refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J96

1j96


Resolution: 1.59→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.29 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.089 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19444 2202 5 %RANDOM
Rwork0.17291 ---
all-44183 --
obs-41981 96.45 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.686 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 75 321 2989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212736
X-RAY DIFFRACTIONr_angle_refined_deg1.252.0013718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3195322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.31515474
X-RAY DIFFRACTIONr_chiral_restr0.0920.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022048
X-RAY DIFFRACTIONr_nbd_refined0.1980.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.233
X-RAY DIFFRACTIONr_mcbond_it0.4591.51619
X-RAY DIFFRACTIONr_mcangle_it0.87122622
X-RAY DIFFRACTIONr_scbond_it1.57131117
X-RAY DIFFRACTIONr_scangle_it2.5964.51096
LS refinement shellResolution: 1.59→1.632 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.204 115
Rwork0.178 2183
obs-1482
Refinement TLS params.Method: refined / Origin x: 13.412 Å / Origin y: 39.494 Å / Origin z: 21.871 Å
111213212223313233
T0.0317 Å2-0.0101 Å2-0.0115 Å2-0.0453 Å20.0025 Å2--0.076 Å2
L0.4103 °2-0.1639 °20.0771 °2-1.1714 °2-0.2237 °2--0.7562 °2
S-0.019 Å °0.0003 Å °-0.0201 Å °-0.0707 Å °0.0345 Å °0.1287 Å °0.0131 Å °0.0063 Å °-0.0155 Å °
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.258

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