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- PDB-6ffb: 17beta-hydroxysteroid dehydrogenase 14 variant S205 - mutant Q148... -

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Basic information

Entry
Database: PDB / ID: 6ffb
Title17beta-hydroxysteroid dehydrogenase 14 variant S205 - mutant Q148A - in complex with a nonsteroidal inhibitor
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / 17b-HSD14 / mutation / inhibition
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
beta-D-glucopyranose / Chem-F45 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionJan 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,8045
Polymers28,6121
Non-polymers1,1924
Water3,873215
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)119,21420
Polymers114,4474
Non-polymers4,76716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
Buried area19820 Å2
ΔGint-192 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.645, 91.645, 132.555
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-505-

HOH

21A-614-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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: 28611.666 Da / Num. of mol.: 1 / Mutation: Q148A
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(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 218 molecules

#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-F45 / [6-(3,4-dihydroxyphenyl)pyridin-2-yl](4-fluoro-3-hydroxyphenyl)methanone


Mass: 325.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FNO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG 6000 20%; Hepes 0.1 M pH 7.00; DMSO 5% / PH range: 7-8

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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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 33549 / % possible obs: 97.7 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rsym value: 0.093 / Net I/σ(I): 13.98
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.92 / Num. unique obs: 5353 / CC1/2: 0.873 / Rsym value: 0.504 / % possible all: 98

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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
Resolution: 1.65→46.335 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.63
RfactorNum. reflection% reflection
Rfree0.175 1678 5 %
Rwork0.1494 --
obs0.1506 33544 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→46.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 81 215 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081987
X-RAY DIFFRACTIONf_angle_d0.9982725
X-RAY DIFFRACTIONf_dihedral_angle_d16.751202
X-RAY DIFFRACTIONf_chiral_restr0.061319
X-RAY DIFFRACTIONf_plane_restr0.007397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6488-1.69740.251360.22112589X-RAY DIFFRACTION97
1.6974-1.75210.2311410.19542670X-RAY DIFFRACTION99
1.7521-1.81480.20871380.1832633X-RAY DIFFRACTION99
1.8148-1.88740.22161390.17022636X-RAY DIFFRACTION99
1.8874-1.97330.19241410.15832672X-RAY DIFFRACTION99
1.9733-2.07740.20081390.15422651X-RAY DIFFRACTION99
2.0774-2.20750.1961410.14882675X-RAY DIFFRACTION99
2.2075-2.3780.17271390.14612642X-RAY DIFFRACTION97
2.378-2.61730.1761390.1412641X-RAY DIFFRACTION98
2.6173-2.99590.15861410.14222673X-RAY DIFFRACTION98
2.9959-3.77430.15181390.14072635X-RAY DIFFRACTION96
3.7743-46.35340.15511450.13792749X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0782-0.03540.00630.094-0.00920.07780.01950.01530.1549-0.06130.0050.061-0.0789-0.060200.1655-0.00350.00050.1382-0.01130.1571-1.6103-18.9507-13.4114
20.0344-0.00770.03150.0097-0.00680.02830.05890.05370.1121-0.17990.0561-0.03380.1318-0.3056-0.00020.21780.0092-0.01310.19510.00560.1679-9.0654-21.4433-25.6256
30.0648-0.0325-0.02420.12-0.0310.0606-0.01880.07970.1477-0.20190.1852-0.27310.0004-0.11160.00180.2389-0.0118-0.01030.1623-0.00450.1476-3.6573-20.4103-25.3825
40.0971-0.00470.02450.1951-0.11980.075-0.06050.0385-0.029-0.15530.02970.0245-0.0097-0.002100.173-0.02320.00650.1610.00450.14830.9463-26.2222-22.1458
50.15340.0951-0.11080.1415-0.04870.0850.13660.06170.0208-0.16390.01570.24340.0319-0.10320.03510.2069-0.0192-0.08090.22250.03580.1672-10.9679-49.8419-24.9585
60.099-0.10950.12480.1465-0.10010.2130.00260.0439-0.0008-0.05340.03420.0067-0.00560.0086-00.1304-0.00840.00660.1349-0.00820.1452.76-36.7726-15.9822
70.0523-0.04080.05480.09170.01930.1163-0.0355-0.13830.1391-0.0120.0161-0.0361-0.0927-0.045500.1409-0.0003-0.00980.1346-0.00280.1656-3.1037-31.601-10.4028
80.08760.0363-0.12740.6931-0.40710.37270.0076-0.0714-0.0436-0.1615-0.06620.25040.3075-0.6254-0.01950.1864-0.0688-0.01410.4489-0.02320.2703-24.5988-36.1254-12.5629
90.0255-0.00170.07470.0052-0.03110.34920.0216-0.0474-0.09880.036-0.0127-0.03830.019-0.075400.12540.0005-0.00050.1390.00940.1289-5.5471-31.3277-2.44
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 212:253)

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