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- PDB-7bw1: Crystal structure of Steroid 5-alpha-reductase 2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7bw1
TitleCrystal structure of Steroid 5-alpha-reductase 2 in complex with Finasteride
Components3-oxo-5-alpha-steroid 4-dehydrogenase 2
KeywordsOXIDOREDUCTASE / Integral membrane protein / Reductase / Steroid
Function / homology
Function and homology information


3-oxo-5alpha-steroid 4-dehydrogenase (NADP+) / biphenyl metabolic process / 3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity / 3-oxo-5-alpha-steroid 4-dehydrogenase activity / dibenzo-p-dioxin metabolic process / phthalate metabolic process / amide binding / female genitalia development / response to follicle-stimulating hormone / Androgen biosynthesis ...3-oxo-5alpha-steroid 4-dehydrogenase (NADP+) / biphenyl metabolic process / 3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity / 3-oxo-5-alpha-steroid 4-dehydrogenase activity / dibenzo-p-dioxin metabolic process / phthalate metabolic process / amide binding / female genitalia development / response to follicle-stimulating hormone / Androgen biosynthesis / androgen biosynthetic process / testosterone biosynthetic process / : / cell body fiber / steroid catabolic process / steroid biosynthetic process / male genitalia development / response to steroid hormone / response to testosterone / hypothalamus development / androgen metabolic process / hippocampus development / response to nutrient levels / response to peptide hormone / bone development / male gonad development / cell-cell signaling / cell differentiation / response to xenobiotic stimulus / neuronal cell body / endoplasmic reticulum membrane
Similarity search - Function
3-oxo-5-alpha-steroid 4-dehydrogenase / 3-oxo-5-alpha-steroid 4-dehydrogenase, C-terminal / 3-oxo-5-alpha-steroid 4-dehydrogenase/very-long-chain enoyl-CoA reductase / 3-oxo-5-alpha-steroid 4-dehydrogenase / Steroid 5-alpha reductase C-terminal domain profile.
Similarity search - Domain/homology
Chem-NDX / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 3-oxo-5-alpha-steroid 4-dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXiao, Q. / Zhang, C. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770791 China
National Natural Science Foundation of China (NSFC)31971131 China
CitationJournal: Res Sq / Year: 2020
Title: Structure of human steroid 5 alpha-reductase 2 with anti-androgen drug finasteride.
Authors: Xiao, Q. / Wang, L. / Supekar, S. / Shen, T. / Liu, H. / Ye, F. / Huang, J. / Fan, H. / Wei, Z. / Zhang, C.
History
DepositionApr 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxo-5-alpha-steroid 4-dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3605
Polymers28,6941
Non-polymers1,6674
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-22 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.449, 107.449, 103.372
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein 3-oxo-5-alpha-steroid 4-dehydrogenase 2 / 5 alpha-SR2 / SR type 2 / Steroid 5-alpha-reductase 2 / S5AR 2 / Type II 5-alpha reductase


Mass: 28693.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRD5A2 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: P31213, 3-oxo-5alpha-steroid 4-dehydrogenase (NADP+)
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-NDX / [[(2~{R},3~{S},4~{R},5~{R})-5-[4-[(1~{S},3~{a}~{S},3~{b}~{S},5~{a}~{R},8~{S},9~{a}~{R},9~{b}~{S},11~{a}~{S})-1-(~{tert}-butylcarbamoyl)-9~{a},11~{a}-dimethyl-7-oxidanylidene-1,2,3,3~{a},3~{b},4,5,5~{a},6,8,9,9~{b},10,11-tetradecahydroindeno[5,4-f]quinolin-8-yl]-3-aminocarbonyl-4~{H}-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 1117.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H66N9O19P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% v/v PEG600, 100mM tris-sodium citrate ph5.0, 100mM sodium chloride, 100mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 9161 / % possible obs: 99.7 % / Redundancy: 9.6 % / Biso Wilson estimate: 68.94 Å2 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.079 / Rrim(I) all: 0.261 / Χ2: 1.131 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.856.81.2744360.4150.5151.380.474100
2.85-2.96.71.1524530.6590.4741.250.503100
2.9-2.968.31.5314420.5930.5281.6250.491100
2.96-3.028.81.2944280.6630.4321.3690.597.7
3.02-3.0810.11.274510.7340.3961.3340.51999.8
3.08-3.1510.31.184500.8210.3591.2370.565100
3.15-3.2310.21.0344410.7840.3241.0870.59100
3.23-3.329.90.8324580.9090.2640.8760.606100
3.32-3.4210.70.6924400.920.2080.7250.639100
3.42-3.5310.80.5484460.9490.1650.5740.69100
3.53-3.6510.50.4474560.9530.1360.4690.804100
3.65-3.810.40.3414520.9590.1050.3580.959100
3.8-3.979.80.2884580.9740.0920.3041.18998.9
3.97-4.1810.40.2344610.9810.0720.2461.352100
4.18-4.449.70.1914570.9830.0610.2011.67199.8
4.44-4.7910.50.1574600.9870.0480.1641.929100
4.79-5.27100.1454690.9930.0440.1522.169100
5.27-6.039.40.1554770.9890.050.1641.756100
6.03-7.589.60.1214900.9940.040.1281.85499.8
7.58-408.50.0835360.9990.0320.092.64799.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35.171 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.2
RfactorNum. reflection% reflection
Rfree0.2646 473 5.17 %
Rwork0.2391 --
obs0.2406 9155 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.8 Å2 / Biso mean: 75.84 Å2 / Biso min: 39.23 Å2
Refinement stepCycle: final / Resolution: 2.8→35.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 110 0 2036
Biso mean--66.5 --
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032107
X-RAY DIFFRACTIONf_angle_d0.7652881
X-RAY DIFFRACTIONf_chiral_restr0.032310
X-RAY DIFFRACTIONf_plane_restr0.004350
X-RAY DIFFRACTIONf_dihedral_angle_d12.902769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-3.1850.33581260.2966273195
3.185-4.01180.27241570.25312898100
4.0118-35.1710.25111900.21963053100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1226-2.24320.65977.47821.74460.9887-0.1604-0.74090.37320.67280.8475-0.0205-0.36191.0998-0.70740.53490.03670.10640.71990.01670.5411-22.063610.676633.7347
23.180.0964-1.51443.15830.28093.2868-0.06380.3617-0.0248-0.8240.08470.2007-0.6971-0.0082-0.03090.6125-0.0019-0.13440.50540.03530.4389-33.555317.246524.3089
33.76580.8886-0.21054.11481.42994.88180.05540.01970.0172-0.2388-0.0508-0.03770.5997-0.16640.06420.5512-0.015-0.10610.38-0.04060.4045-37.58396.417136.0828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 48 )A5 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 180 )A49 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 254 )A181 - 254

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