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- PDB-3gug: Crystal structure of AKR1C1 L308V mutant in complex with NADP and... -

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Basic information

Entry
Database: PDB / ID: 3gug
TitleCrystal structure of AKR1C1 L308V mutant in complex with NADP and 3,5-dichlorosalicylic acid
ComponentsAldo-keto reductase family 1 member C1
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / 20 alpha hydroxysteroid dehydrogenase / AKR1C1 / Cytoplasm / NADP / Polymorphism
Function / homology
Function and homology information


3-beta-hydroxy-5-beta-steroid dehydrogenase (NADP+) activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] 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 activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase ...3-beta-hydroxy-5-beta-steroid dehydrogenase (NADP+) activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] 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 activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / 5-alpha-androstane-3-beta,17-beta-diol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase [NAD(P)+] activity / testosterone dehydrogenase (NADP+) activity / ketosteroid monooxygenase activity / intestinal cholesterol absorption / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / retinal metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / : / bile acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / bile acid binding / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / Prednisone ADME / prostaglandin metabolic process / bile acid and bile salt transport / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoid metabolic process / 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
3,5-dichloro-2-hydroxybenzoic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDhagat, U. / El-Kabbani, O.
CitationJournal: To be Published
Title: Crystal structure of AKR1C1 L308V mutant in complex with NADP and 3,5-dichlorosalicylic acid
Authors: Dhagat, U. / Hara, A. / El-Kabbani, O.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,8414
Polymers36,8251
Non-polymers1,0163
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.412, 83.885, 48.914
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase family 1 member C1 / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD


Mass: 36825.305 Da / Num. of mol.: 1 / Mutation: L308V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C1, DDH, DDH1 / Plasmid: pKK223-3, pKKDD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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-C2U / 3,5-dichloro-2-hydroxybenzoic acid


Mass: 207.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4Cl2O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 43.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 25% Polyethylene glycol monomethyl ether 550, 0.01M Zinc sulphate heptahydrate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2008 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 24030 / Num. obs: 22733 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.01 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.81 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2237 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C3U

3c3u


Resolution: 1.9→29.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.655 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.195 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, Ser 221 is in the disallowed regions because its main chain H-bonds with the cofactor
RfactorNum. reflection% reflectionSelection details
Rfree0.26021 1216 5.1 %RANDOM
Rwork0.19041 ---
obs0.19392 22522 94.62 %-
all-24030 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.165 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å2-1.11 Å2
2--2.31 Å20 Å2
3----0.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 61 318 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222671
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9993632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1335321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93524.132121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16815460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0021517
X-RAY DIFFRACTIONr_chiral_restr0.1610.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022019
X-RAY DIFFRACTIONr_nbd_refined0.20.21347
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2237
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.224
X-RAY DIFFRACTIONr_mcbond_it1.0571.51674
X-RAY DIFFRACTIONr_mcangle_it1.47222593
X-RAY DIFFRACTIONr_scbond_it2.58731184
X-RAY DIFFRACTIONr_scangle_it3.5614.51037
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 96 -
Rwork0.303 1654 -
obs-2379 94.04 %

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