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- PDB-9av4: Design and application of synthetic 17B-HSD13 substrates to drug ... -

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Basic information

Entry
Database: PDB / ID: 9av4
TitleDesign and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants
ComponentsHydroxysteroid 17-beta dehydrogenase 13
KeywordsHYDROLASE / enzyme / substrate / HSd17B13
Function / homology17beta-estradiol 17-dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17beta-estradiol 17-dehydrogenase
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLiu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Design and application of synthetic 17B-HSD13 substrates reveals preserved catalytic activity of protective human variants.
Authors: Garnsey, M.R. / Wang, Y. / Edmonds, D.J. / Sammons, M.F. / Reidich, B. / Ahn, Y. / Ashkenazi, Y. / Carlo, A. / Cerny, M.A. / Coffman, K.J. / Culver, J.A. / Dechert Schmitt, A.M. / Eng, H. / ...Authors: Garnsey, M.R. / Wang, Y. / Edmonds, D.J. / Sammons, M.F. / Reidich, B. / Ahn, Y. / Ashkenazi, Y. / Carlo, A. / Cerny, M.A. / Coffman, K.J. / Culver, J.A. / Dechert Schmitt, A.M. / Eng, H. / Fisher, E.L. / Gutierrez, J.A. / James, L. / Jordan, S. / Kohrt, J.T. / Kramer, M. / LaChapelle, E.A. / Lee, J.C. / Lee, J. / Li, D. / Li, Z. / Liu, S. / Liu, J. / Magee, T.V. / Miller, M.R. / Moran, M. / Nason, D.M. / Nedoma, N.L. / O'Neil, S.V. / Piotrowski, M.A. / Racich, J. / Sommese, R.F. / Stevens, L.M. / Wright, A.S. / Xiao, J. / Zhang, L. / Zhou, D. / Barrandon, O. / Clasquin, M.F.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxysteroid 17-beta dehydrogenase 13
B: Hydroxysteroid 17-beta dehydrogenase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7556
Polymers70,7002
Non-polymers2,0554
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-45 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.97, 76.06, 65.24
Angle α, β, γ (deg.)90, 94.69, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hydroxysteroid 17-beta dehydrogenase 13


Mass: 35350.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Dog HSD17B13 with 4 mutations to make it more human enzyme-like
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B13, HSD17B11 / Production host: Insect BA phytoplasma (bacteria) / References: UniProt: A0A8C0PP93
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-A1AG4 / 4-(3,4-dichlorobenzene-1-sulfonamido)-2-fluorobenzoic acid


Mass: 364.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8Cl2FNO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein was incubated at 12 mg/ml with 1 mM NAD+ and 1 mM compound 1 with the addition of 0.125% beta-octyl-glucoside. Sitting drop vapor diffusion crystallization was set up by mixing 300 ...Details: protein was incubated at 12 mg/ml with 1 mM NAD+ and 1 mM compound 1 with the addition of 0.125% beta-octyl-glucoside. Sitting drop vapor diffusion crystallization was set up by mixing 300 nl protein complex with 300 nl of reservoir solution containing 30% PEG3350, 0.2 M ammonium chloride. Crystals grew at room temperature over 2 weeks.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→93.17 Å / Num. obs: 28362 / % possible obs: 87.9 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Net I/σ(I): 11.9
Reflection shellResolution: 2.09→2.36 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2 / Num. unique obs: 1419 / CC1/2: 0.763 / Rpim(I) all: 0.33 / % possible all: 56.2

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→33.47 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 1410 -RANDOM
Rwork0.2113 ---
obs0.2126 28372 46.5 %-
Displacement parametersBiso mean: 45.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.9579 Å20 Å20.3583 Å2
2--0.9125 Å20 Å2
3----6.8704 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.09→33.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 132 56 4128
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084190HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.945709HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1439SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes733HARMONIC5
X-RAY DIFFRACTIONt_it4176HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion570SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3172SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion18.34
LS refinement shellResolution: 2.09→2.21 Å
RfactorNum. reflection% reflection
Rfree0.3371 33 -
Rwork0.3041 --
obs--3.67 %
Refinement TLS params.

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)
11.232-0.1133-0.16032.26460.45355.0218-0.0148-0.11550.2857-0.11550.0332-0.540.2857-0.54-0.0185-0.1042-0.0316-0.0019-0.10990.0302-0.232331.7688-37.1811-6.2274
21.4850.5113-0.28121.84030.06773.61590.02490.158-0.52520.158-0.0034-0.52-0.5252-0.52-0.0215-0.01370.11050.0474-0.09770.0124-0.25529.8582-19.77119.0559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A14 - 273
2X-RAY DIFFRACTION1{ A|* }A296 - 301
3X-RAY DIFFRACTION2{ B|* }B25 - 272
4X-RAY DIFFRACTION2{ B|* }B296 - 301

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