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- PDB-2p5n: Crystal structure of mouse 17-alpha hydroxysteroid dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 2p5n
TitleCrystal structure of mouse 17-alpha hydroxysteroid dehydrogenase in complex with coenzyme NADPH
ComponentsAldo-keto reductase family 1, member C21
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / Hydroxysteroid Dehydrogenase / Binary Complex / TIM barrel
Function / homology
Function and homology information


Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase activity / chlordecone reductase activity / Retinoid metabolism and transport / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / C21-steroid hormone metabolic process / 3(or 17)alpha-hydroxysteroid dehydrogenase / 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 activity / chlordecone reductase activity / Retinoid metabolism and transport / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / C21-steroid hormone metabolic process / 3(or 17)alpha-hydroxysteroid dehydrogenase / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / steroid dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / alcohol 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 / progesterone metabolic process / : / 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 / prostaglandin metabolic process / steroid metabolic process / NADPH binding / steroid binding / oxidoreductase activity / 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
Chem-NDP / Aldo-keto reductase family 1 member C21 / Aldo-keto reductase family 1 member C21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEl-Kabbani, O. / Dhagat, U.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) holoenzyme from an orthorhombic crystal form: an insight into the bifunctionality of the enzyme.
Authors: Dhagat, U. / Carbone, V. / Chung, R.P. / Schulze-Briese, C. / Endo, S. / Hara, A. / El-Kabbani, O.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Oct 25, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE IS A DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THIS IS A VARIANT.

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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)75,5766
Polymers73,8492
Non-polymers1,7274
Water10,251569
1
A: Aldo-keto reductase family 1, member C21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7883
Polymers36,9251
Non-polymers8642
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)37,7883
Polymers36,9251
Non-polymers8642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.910, 84.900, 95.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 / AKR1C21


Mass: 36924.578 Da / Num. of mol.: 2
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: Q6P8V0, UniProt: Q91WR5*PLUS
#2: 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
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 10% PEG 6000, 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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 15, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 64907 / Num. obs: 59131 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.8→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.475 / Num. unique all: 14752 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MRQ

1mrq


Resolution: 1.8→12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.341 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.159 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26796 3009 5.1 %RANDOM
Rwork0.19781 ---
obs0.20136 55952 91.3 %-
all-64907 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---2.1 Å20 Å2
3---0.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.241 Å
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 112 569 5865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225452
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9957406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9815654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14724.39246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86615960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0471528
X-RAY DIFFRACTIONr_chiral_restr0.1270.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024070
X-RAY DIFFRACTIONr_nbd_refined0.2170.22708
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2481
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.222
X-RAY DIFFRACTIONr_mcbond_it0.9961.53350
X-RAY DIFFRACTIONr_mcangle_it1.52325247
X-RAY DIFFRACTIONr_scbond_it2.43532427
X-RAY DIFFRACTIONr_scangle_it3.4784.52154
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2569 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.390.5
medium thermal1.632
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 227 -
Rwork0.308 3604 -
obs--82.42 %

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