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- PDB-6mne: CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TY... -

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Basic information

Entry
Database: PDB / ID: 6mne
TitleCRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRONE AND NADP+
ComponentsEstradiol 17-beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE / 17BETA-HSD1 / ESTRONE / FUNCTIONAL ANALYSES
Function / homology
Function and homology information


estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
17beta-dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J3Z / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
Model details17beta-HSD1-E1-NADP+ complex
AuthorsLi, T. / Lin, S.X.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structures of human 17 beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NADP+reveal the mechanism of substrate inhibition.
Authors: Li, T. / Stephen, P. / Zhu, D.W. / Shi, R. / Lin, S.X.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estradiol 17-beta-dehydrogenase 1
B: Estradiol 17-beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0987
Polymers69,9782
Non-polymers2,1205
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-33 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.780, 108.240, 117.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estradiol 17-beta-dehydrogenase 1 / 17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / 20 alpha-hydroxysteroid dehydrogenase ...17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / 20 alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH / Placental 17-beta-hydroxysteroid dehydrogenase / Short chain dehydrogenase/reductase family 28C member 1


Mass: 34989.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B1, E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9
References: UniProt: P14061, 17beta-estradiol 17-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-J3Z / (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one / Estrone


Mass: 270.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O2 / Comment: hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.99 Å3/Da / Density % sol: 38.33 % / Mosaicity: 0.26 °
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: KH2PO4, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→49.17 Å / Num. obs: 47986 / % possible obs: 100 % / Redundancy: 7.4 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Rsym value: 0.084 / Net I/av σ(I): 5.1 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.86-1.967.40.481.469110.1880.5160.48100
1.96-2.087.40.2862.565410.1120.3080.286100
2.08-2.227.40.1983.561390.0770.2120.198100
2.22-2.47.40.1514.557650.0590.1620.151100
2.4-2.637.40.1215.352880.0480.130.121100
2.63-2.947.40.08848310.0310.0860.08100
2.94-3.47.40.095.942890.0350.0970.09100
3.4-4.167.30.0757.536420.030.0810.075100
4.16-5.887.20.0510.828810.020.0540.05100
5.88-106.70.0441116990.0180.0480.04499.9

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Processing

Software
NameVersionClassification
MOSFLM7.2.0data reduction
SCALA3.3.22data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
MOLREP11.4.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JTV

1jtv


Resolution: 1.86→49.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.181 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1494 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 2457 5.1 %RANDOM
Rwork0.1938 ---
obs0.1953 45454 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.83 Å2 / Biso mean: 31.634 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å2-0 Å2
2---1.86 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.86→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 108 128 4484
Biso mean--43.71 29.47 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194495
X-RAY DIFFRACTIONr_bond_other_d0.0010.024371
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.0136127
X-RAY DIFFRACTIONr_angle_other_deg0.933310027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04822.108185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08415734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0941547
X-RAY DIFFRACTIONr_chiral_restr0.0770.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021023
LS refinement shellResolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 174 -
Rwork0.245 3345 -
all-3519 -
obs--99.97 %

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