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- PDB-6gbt: 17beta-hydroxysteroid dehydrogenase type 14 Mutant Y253A in compl... -

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Basic information

Entry
Database: PDB / ID: 6gbt
Title17beta-hydroxysteroid dehydrogenase type 14 Mutant Y253A in complex with a non-steroidal inhibitor
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / Inhibitor Complex mutant
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
Chem-F45 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-fucose dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBadran, M. / Klebe, G. / Heine, A. / Marchais-Oberwinkler, S.
CitationJournal: To Be Published
Title: 17beta Hydroxysteroid Dehydrogenase type 14 mutant C255A in complex with non-steroidal inhibitor
Authors: Badran, M.J.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,3875
Polymers28,2971
Non-polymers1,0904
Water2,864159
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)117,54920
Polymers113,1894
Non-polymers4,35916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area21210 Å2
ΔGint-179 kcal/mol
Surface area31900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.654, 91.654, 134.099
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-434-

HOH

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Components

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Protein , 1 types, 1 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: 28297.330 Da / Num. of mol.: 1 / Mutation: C255A
Source method: isolated from a genetically manipulated source
Details: Wild type S205 PubMed:10800688mutation Cys255Ala / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 163 molecules

#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: 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
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG6000 50% W/V HEPES 0.1M DMSO 5% / PH range: 6.5 - 7.5

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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: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17086 / % possible obs: 99.4 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rrim(I) all: 0.093 / Rsym value: 0.087 / Net I/σ(I): 20.84
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 9 % / Mean I/σ(I) obs: 4.75 / Num. unique obs: 2653 / CC1/2: 0.928 / Rrim(I) all: 0.506 / Rsym value: 0.477 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5icm

5icm


Resolution: 2.1→46.5989 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.31
RfactorNum. reflection% reflection
Rfree0.1904 854 5 %
Rwork0.1497 --
obs0.1518 17073 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.5989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 73 159 2074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091976
X-RAY DIFFRACTIONf_angle_d0.8612701
X-RAY DIFFRACTIONf_dihedral_angle_d18.751198
X-RAY DIFFRACTIONf_chiral_restr0.054313
X-RAY DIFFRACTIONf_plane_restr0.005392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.22630.23711370.16112597X-RAY DIFFRACTION98
2.2263-2.39810.2231410.15852671X-RAY DIFFRACTION100
2.3981-2.63940.22991400.15472672X-RAY DIFFRACTION100
2.6394-3.02130.23051430.15342705X-RAY DIFFRACTION100
3.0213-3.8060.17131430.14482731X-RAY DIFFRACTION100
3.806-40.18370.15891500.14512843X-RAY DIFFRACTION99

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