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- PDB-5hs6: Human 17beta-hydroxysteroid dehydrogenase type 14 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5hs6
TitleHuman 17beta-hydroxysteroid dehydrogenase type 14 in complex with Estrone
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / 17bHSD14 / Estrone complex
Function / homology
Function and homology information


Estrogen biosynthesis / estradiol 17-beta-dehydrogenase [NAD(P)] activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsBertoletti, N. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationKL1204/15-1 Germany
German Research FoundationMA-5287/1-1
CitationJournal: J.Med.Chem. / Year: 2016
Title: New Insights into Human 17 beta-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor.
Authors: Bertoletti, N. / Braun, F. / Lepage, M. / Moller, G. / Adamski, J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionJan 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6404
Polymers28,6831
Non-polymers9573
Water2,450136
1
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,55816
Polymers114,7314
Non-polymers3,82712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area21790 Å2
ΔGint-206 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.111, 91.111, 132.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-536-

HOH

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Components

#1: Protein 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family ...17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1


Mass: 28682.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#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 / Comment: hormone*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: CHES 0.1M, tri-sodium citrate 1M / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 18613 / % possible obs: 99.7 % / Redundancy: 7.52 % / Rsym value: 0.083 / Net I/σ(I): 15.86
Reflection shellResolution: 2.02→2.14 Å / Redundancy: 7.57 % / Mean I/σ(I) obs: 4.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4

5en4


Resolution: 2.02→46.106 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.1877 931 5 %
Rwork0.1599 --
obs0.1614 18611 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→46.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 64 136 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071969
X-RAY DIFFRACTIONf_angle_d0.8682692
X-RAY DIFFRACTIONf_dihedral_angle_d19.1191189
X-RAY DIFFRACTIONf_chiral_restr0.054315
X-RAY DIFFRACTIONf_plane_restr0.005375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0184-2.12480.24011290.19082450X-RAY DIFFRACTION99
2.1248-2.25790.2081300.1752478X-RAY DIFFRACTION100
2.2579-2.43230.20361320.16712499X-RAY DIFFRACTION100
2.4323-2.6770.19811320.16612505X-RAY DIFFRACTION100
2.677-3.06430.19461320.16912512X-RAY DIFFRACTION100
3.0643-3.86040.18081340.15122556X-RAY DIFFRACTION100
3.8604-46.11780.1681420.14892680X-RAY DIFFRACTION100
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)
18.97233.81633.60945.39851.59794.4380.0375-0.25650.2422-0.0071-0.09730.0273-0.276-0.11580.05720.19330.02680.02540.11740.02140.141443.942126.5641-13.3849
26.3458-5.9117-4.78358.36755.97986.26190.30140.3030.0929-0.412-0.1579-0.086-0.0867-0.5881-0.11750.23460.0065-0.04470.23280.03320.161438.769526.7648-24.2078
34.76463.5427-0.51633.5605-0.85742.4601-0.15250.3086-0.0198-0.37930.1660.16240.08140.0653-0.0250.25270.0378-0.00030.158-0.01760.172948.715420.9741-23.6743
40.88040.7192-0.08252.2788-0.04251.12670.01920.10380.0305-0.2210.01720.09090.0076-0.0303-0.03570.21150.0304-0.00650.18880.00390.183845.77477.4034-16.4407
57.9636-0.26783.19022.6481-0.86766.6242-0.09760.07450.025-0.28870.05280.30860.1487-0.83630.05740.18980.00730.00360.3464-0.01140.288524.402311.5095-9.4557
64.58970.1626-0.92370.8771-1.25772.3080.06860.0682-0.0765-0.0046-0.0742-0.0865-0.0231-0.00580.0080.19680.00340.00230.1634-0.04090.166143.071914.1809-2.4972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:39)
2X-RAY DIFFRACTION2(chain A and resid 40:63)
3X-RAY DIFFRACTION3(chain A and resid 64:93)
4X-RAY DIFFRACTION4(chain A and resid 94:185)
5X-RAY DIFFRACTION5(chain A and resid 186:220)
6X-RAY DIFFRACTION6(chain A and resid 221:254)

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