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- PDB-6hno: 17beta-hydroxysteroid dehydrogenase 14 variant S205 - mutant H93A -

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Basic information

Entry
Database: PDB / ID: 6hno
Title17beta-hydroxysteroid dehydrogenase 14 variant S205 - mutant H93A
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / 17b-HSD14 / mutation / inhibition
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase / D-threo-aldose 1-dehydrogenase activity / Estrogen biosynthesis / L-fucose catabolic process / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-fucose dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBertoletti, N. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationMA-5287/1-1 Germany
German Research FoundationKL-1204/15-1 Germany
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2019
Title: Mutational and structural studies uncover crucial amino acids determining activity and stability of 17 beta-HSD14.
Authors: Badran, M.J. / Bertoletti, N. / Keils, A. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2652
Polymers28,6021
Non-polymers6631
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.400, 91.400, 132.696
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-448-

HOH

21A-575-

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: 28601.650 Da / Num. of mol.: 1 / Mutation: H93A
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


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 6000 20%; Hepes 0.1 M pH 7.00; DMSO 5%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 31576 / % possible obs: 97.5 % / Redundancy: 8.22 % / Biso Wilson estimate: 18.255 Å2 / Rsym value: 0.058 / Net I/σ(I): 23.2
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.96 / Num. unique obs: 5144 / Rsym value: 0.502 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICM

5icm


Resolution: 1.68→30.02 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.41
RfactorNum. reflection% reflection
Rfree0.205 1571 4.99 %
Rwork0.1681 --
obs0.1699 31491 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 44 191 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091940
X-RAY DIFFRACTIONf_angle_d1.0382658
X-RAY DIFFRACTIONf_dihedral_angle_d16.8041167
X-RAY DIFFRACTIONf_chiral_restr0.059314
X-RAY DIFFRACTIONf_plane_restr0.007368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6794-1.73360.28721430.21472724X-RAY DIFFRACTION99
1.7336-1.79560.22811450.18772761X-RAY DIFFRACTION100
1.7956-1.86740.22361450.18612742X-RAY DIFFRACTION100
1.8674-1.95240.47841170.34252260X-RAY DIFFRACTION82
1.9524-2.05530.171450.16552761X-RAY DIFFRACTION100
2.0553-2.18410.17971460.14972773X-RAY DIFFRACTION100
2.1841-2.35260.26311290.21052484X-RAY DIFFRACTION89
2.3526-2.58930.17121480.15072796X-RAY DIFFRACTION100
2.5893-2.96370.20051470.15612811X-RAY DIFFRACTION100
2.9637-3.73280.16611500.15212834X-RAY DIFFRACTION100
3.7328-30.02460.19651560.14882974X-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)
10.1993-0.06230.20630.0551-0.03680.22440.02380.00890.0632-0.0401-0.0020.0486-0.0973-0.0167-00.199-0.00270.02650.1491-0.01960.1699-1.6576-18.9792-13.322
20.0109-0.0078-0.00030.0511-0.03410.02490.05360.2849-0.01260.1507-0.1207-0.45390.1525-0.47360.00030.22120.00170.01260.2866-0.01510.2256-8.9299-20.903-24.8412
30.4162-0.2-0.01680.0960.00270.00510.01780.04250.2322-0.33460.1651-0.1210.0001-0.15850.03930.2939-0.0017-0.00810.2039-0.02540.2108-3.937-20.1112-25.0251
40.1942-0.12720.07020.4594-0.11680.02970.02890.0503-0.0352-0.1262-0.01860.1272-0.04070.0394-0.00020.2224-0.0096-0.00010.202-0.00890.17521.429-25.8737-22.361
50.66570.0686-0.23070.510.41730.46620.03310.47230.1088-0.20240.26330.1735-0.1046-0.1730.39230.31760.0167-0.14340.25330.02550.2338-10.8378-49.443-25.2494
60.04290.10520.08020.6661-0.02180.23030.0357-0.00170.048-0.1166-0.01430.0617-0.01080.015100.17910.01310.01180.1547-0.00160.18352.7527-36.6402-15.7038
70.11050.06140.00850.14440.14110.1786-0.3481-0.01270.2413-0.18360.17890.04730.031-0.0913-0.0040.18-0.0306-0.01230.16760.01260.1908-2.9166-31.5046-10.1259
80.0164-0.0418-0.00410.11090.00470.02830.01890.0819-0.0418-0.489-0.25430.39310.1684-0.02670.00140.3981-0.0972-0.09550.6147-0.01340.521-24.7452-36.2908-11.969
90.1426-0.0256-0.06670.2371-0.34180.56450.0416-0.0376-0.02040.022-0.02560.06840.0172-0.0893-00.1807-0.00230.02340.1694-0.00170.1716-5.7185-31.5962-2.2843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:37)
2X-RAY DIFFRACTION2(chain A and resid 38:49)
3X-RAY DIFFRACTION3(chain A and resid 50:67)
4X-RAY DIFFRACTION4(chain A and resid 68:97)
5X-RAY DIFFRACTION5(chain A and resid 98:109)
6X-RAY DIFFRACTION6(chain A and resid 110:174)
7X-RAY DIFFRACTION7(chain A and resid 175:191)
8X-RAY DIFFRACTION8(chain A and resid 192:211)
9X-RAY DIFFRACTION9(chain A and resid 212:254)

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