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

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Basic information

Entry
Database: PDB / ID: 6mnc
TitleCRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRONE
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 dehydrogenase (NAD+) activity / testosterone biosynthetic process ...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 dehydrogenase (NAD+) activity / testosterone biosynthetic process / 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 / adipose tissue development / skeletal muscle tissue development / catalytic activity / steroid binding / bone development / gene expression / NADP binding / protein homodimerization activity / cytosol / cytoplasm
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 / DI(HYDROXYETHYL)ETHER / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
Model details17beta-HSD1-E1 complex
AuthorsLi, T. / Stephen, P. / Zhu, D.W. / 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)70,3544
Polymers69,9782
Non-polymers3762
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-34 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.560, 110.020, 117.140
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 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-J3Z / (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one / Estrone / Estrone


Mass: 270.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.01 Å3/Da / Density % sol: 38.74 % / Mosaicity: 1.18 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: MgCl2, PEG3350, Glycerol

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.01 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.4→49.793 Å / Num. obs: 21966 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Rsym value: 0.056 / Net I/av σ(I): 7.6 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.4-2.533.10.4581.729550.2870.5430.45891.7
2.53-2.683.10.3352.328920.2110.3980.33593.5
2.68-2.873.10.2123.627850.1340.2520.21295.7
2.87-3.13.30.145.326340.0860.1650.1496.8
3.1-3.393.60.0868.224650.0510.10.08698.4
3.39-3.7940.05711.222780.0320.0660.05799.6
3.79-4.384.20.04214.120540.0230.0480.04299.8
4.38-5.374.20.03416.617290.0190.0390.03499.7
5.37-7.594.10.0414.513580.0220.0460.0499.5
7.59-49.7933.80.0439.58160.0250.050.04398.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.608
Highest resolutionLowest resolution
Rotation49.79 Å2.71 Å

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Processing

Software
NameVersionClassification
MOSFLM7.0.9data reduction
SCALA3.3.22data scaling
MOLREP11.4.05phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
Coot0.8.7model building
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JTV

1jtv


Resolution: 2.4→49.79 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.141 / SU ML: 0.254 / SU R Cruickshank DPI: 0.5428 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.321
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 1123 5.1 %RANDOM
Rwork0.2071 ---
obs0.2113 20806 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.32 Å2 / Biso mean: 57.524 Å2 / Biso min: 20.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--0.39 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 2.4→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 27 9 4250
Biso mean--60.75 35.86 -
Num. residues----552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194325
X-RAY DIFFRACTIONr_bond_other_d0.0020.024236
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.995871
X-RAY DIFFRACTIONr_angle_other_deg1.12739708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8855548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39122.36178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25315708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0881542
X-RAY DIFFRACTIONr_chiral_restr0.1050.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214839
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 78 -
Rwork0.296 1403 -
all-1481 -
obs--90.3 %

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