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- PDB-3fjn: The crystal structure of 17-alpha hydroxysteroid dehydrogenase Y2... -

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Basic information

Entry
Database: PDB / ID: 3fjn
TitleThe crystal structure of 17-alpha hydroxysteroid dehydrogenase Y224D mutant.
ComponentsAldo-keto reductase family 1 member C21
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / 17-alpha-hydroxysteroid dehydrogenase / Cytoplasm / Lipid metabolism / NADP / Phosphoprotein / Steroid metabolism
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
ACETATE ION / Aldo-keto reductase family 1 member C21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDhagat, U. / El-Kabbani, O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme
Authors: Dhagat, U. / Endo, S. / Mamiya, H. / Hara, A. / El-Kabbani, O.
History
DepositionDec 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: 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 ...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.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)73,9896
Polymers73,7532
Non-polymers2364
Water9,242513
1
A: Aldo-keto reductase family 1 member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9953
Polymers36,8761
Non-polymers1182
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)36,9953
Polymers36,8761
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.317, 97.837, 69.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 7 - 323 / Label seq-ID: 7 - 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: 36876.492 Da / Num. of mol.: 2 / Mutation: Y224D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / 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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 44.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.2M Magnesium Acetate, 20% Polyethylene glycol8000, pH 6.5, 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: Sep 4, 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: 2.3→30 Å / Num. obs: 28098 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.34 % / Rmerge(I) obs: 0.0552 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.1343 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2085 / % possible all: 94.7

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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 2P5N

2p5n


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.443 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.422 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. SOME OF WATERS LISTED IN REMARK 525 ARE FITTED CLOSE TO THE GENERATED SYMMETRY ATOMS OF THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.27682 1490 5.1 %RANDOM
Rwork0.17394 ---
obs0.1791 27772 98.84 %-
all-28224 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.61 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5095 0 16 513 5624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225229
X-RAY DIFFRACTIONr_angle_refined_deg2.1891.9717076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.2325637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7924.477239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1115932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5871526
X-RAY DIFFRACTIONr_chiral_restr0.160.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023946
X-RAY DIFFRACTIONr_nbd_refined0.2230.22522
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2359
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.215
X-RAY DIFFRACTIONr_mcbond_it1.1531.53295
X-RAY DIFFRACTIONr_mcangle_it1.87925151
X-RAY DIFFRACTIONr_scbond_it3.05932226
X-RAY DIFFRACTIONr_scangle_it4.5324.51923
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2471 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.330.5
medium thermal1.752
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 105 -
Rwork0.185 1936 -
obs--94.45 %

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