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- PDB-3cv6: The crystal structure of mouse 17-alpha hydroxysteroid dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 3cv6
TitleThe crystal structure of mouse 17-alpha hydroxysteroid dehydrogenase GG225.226PP mutant in complex with inhibitor and cofactor NADP+.
ComponentsAldo-keto reductase family 1 member C21
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / Hydroxysteroid Dehydrogenase / Ternary Complex / Hexestrol / Lipid metabolism / NADP / Phosphoprotein / Steroid metabolism
Function / homology
Function and homology information


Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase (NADPH) activity / RA biosynthesis pathway / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Retinoid metabolism and transport / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol ...Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase (NADPH) activity / RA biosynthesis pathway / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Retinoid metabolism and transport / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Prednisone ADME / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / 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 / NADP+ binding / aldose reductase (NADPH) activity / 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-HXS / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDhagat, U. / El-Kabbani, O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the G225P/G226P mutant of mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) ternary complex: implications for the binding of inhibitor and substrate.
Authors: Dhagat, U. / Endo, S. / Mamiya, H. / Hara, A. / El-Kabbani, O.
History
DepositionApr 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 13, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)76,42811
Polymers74,0092
Non-polymers2,4189
Water11,962664
1
A: Aldo-keto reductase family 1 member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1755
Polymers37,0051
Non-polymers1,1704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo-keto reductase family 1 member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2536
Polymers37,0051
Non-polymers1,2485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.108, 102.108, 72.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 1 - 323 / Label seq-ID: 1 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aldo-keto reductase family 1 member C21 / 17-alpha-hydroxysteroid dehydrogenase / 17-alpha-HSD / 3-alpha-hydroxysteroid dehydrogenase / ...17-alpha-hydroxysteroid dehydrogenase / 17-alpha-HSD / 3-alpha-hydroxysteroid dehydrogenase / Dihydrodiol dehydrogenase type 1 / DD1 / Dihydrodiol dehydrogenase type 3 / DD3


Mass: 37004.707 Da / Num. of mol.: 2 / Mutation: G225P, G226P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c21 / Plasmid: pkk223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q91WR5, 3(or 17)alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-HXS / 4-[(1R,2S)-1-ethyl-2-(4-hydroxyphenyl)butyl]phenol


Mass: 270.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O2
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THIS IS A VARIANT AT THESE ...THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THIS IS A VARIANT AT THESE POSITIONS. THR221 IN MOLECULES A AND B MAKES CLOSE CONTACTS WITH THE COENZYME RESULTING IN A DEVIATION IN CHIRALITY.

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 10% PEG l6000, 5% 2-methyl-2,4-pentanediol, pH 7.5, 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: Jan 17, 2007 / 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: 2.1→30 Å / Num. all: 46728 / Num. obs: 46635 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.01 % / Rmerge(I) obs: 0.0392 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.3672 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p5n

2p5n


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.418 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.221 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25611 2487 5.1 %RANDOM
Rwork0.19733 ---
obs0.20028 46635 99.85 %-
all-46728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 156 664 6016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225600
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.0017616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9495678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92724.263251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59815987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9391530
X-RAY DIFFRACTIONr_chiral_restr0.120.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024200
X-RAY DIFFRACTIONr_nbd_refined0.2010.22566
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2456
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.218
X-RAY DIFFRACTIONr_mcbond_it0.7781.53432
X-RAY DIFFRACTIONr_mcangle_it1.24525360
X-RAY DIFFRACTIONr_scbond_it1.99232532
X-RAY DIFFRACTIONr_scangle_it2.9314.52241
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2619 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.230.5
medium thermal0.412
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 191 -
Rwork0.32 3451 -
obs--100 %

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