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

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Basic information

Entry
Database: PDB / ID: 6dtp
TitleCRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH EM139
ComponentsEstradiol 17-beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE/Inhibitor / 17BETA-HSD1 / OXIDOREDUCTASE / STEROID / inhibitor / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / cellular response to metal ion / estrogen biosynthetic process / estradiol binding / Estrogen biosynthesis / testosterone dehydrogenase (NADP+) activity / testosterone biosynthetic process / : / testosterone dehydrogenase (NAD+) activity ...17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / cellular response to metal ion / estrogen biosynthetic process / estradiol binding / Estrogen biosynthesis / testosterone dehydrogenase (NADP+) activity / testosterone biosynthetic process / : / testosterone dehydrogenase (NAD+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / small molecule binding / The canonical retinoid cycle in rods (twilight vision) / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / 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-EM9 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
Model details17beta-HSD1-EM139 complex
AuthorsLi, T. / Lin, S.X.
CitationJournal: Health / Year: 2018
Title: CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH Dual-Site Inhibitor EM-139
Authors: Li, T. / Zhu, D. / Labrie, F. / Lin, S.X.
History
DepositionJun 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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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)71,68716
Polymers69,9782
Non-polymers1,70914
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-23 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.761, 42.188, 122.671
Angle α, β, γ (deg.)90.000, 102.070, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 82 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EM9 / N-butyl-11-[(7alpha,9beta,13alpha,14beta,16alpha,17alpha)-16-chloro-3,17-dihydroxyestra-1,3,5(10)-trien-7-yl]-N-methylundecanamide


Mass: 560.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H54ClNO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.18 Å3/Da / Density % sol: 43.67 % / Mosaicity: 1.53 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: MgCl2, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2→35.675 Å / Num. obs: 38108 / % possible obs: 92.7 % / Redundancy: 3.6 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Rsym value: 0.073 / Net I/av σ(I): 5.9 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2-2.113.70.2692.455360.1630.3150.26992.5
2.11-2.243.70.2043.151840.1250.240.20492.5
2.24-2.393.60.1484.149080.090.1730.14892.8
2.39-2.583.60.1224.946130.0750.1440.12293.1
2.58-2.833.60.0946.642910.0580.1110.09493.4
2.83-3.163.60.0797.538480.0480.0930.07993.4
3.16-3.653.60.0688.434360.0420.0810.06894.1
3.65-4.473.50.06110.129080.0370.0710.06193.7
4.47-6.323.60.0559.922770.0330.0640.05594
6.32-35.6753.40.04214.211070.0260.050.04280.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.637
Highest resolutionLowest resolution
Rotation35.68 Å2.21 Å

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Processing

Software
NameVersionClassification
MOSFLM6.2.6data reduction
SCALA3.3.22data scaling
MOLREP11.4.05phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jtv

1jtv


Resolution: 2→35.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.57 / SU ML: 0.123 / SU R Cruickshank DPI: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.172
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1961 5.2 %RANDOM
Rwork0.1908 ---
obs0.193 36107 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.03 Å2 / Biso mean: 42.137 Å2 / Biso min: 21.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.74 Å2
2--4.04 Å20 Å2
3----4.56 Å2
Refinement stepCycle: final / Resolution: 2→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 97 68 4418
Biso mean--69.59 39.91 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194460
X-RAY DIFFRACTIONr_bond_other_d0.0020.024388
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9976035
X-RAY DIFFRACTIONr_angle_other_deg0.985310059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02822.216185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10315724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2871545
X-RAY DIFFRACTIONr_chiral_restr0.0820.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021009
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 138 -
Rwork0.262 2609 -
all-2747 -
obs--91.81 %

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