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- PDB-8g89: HSD17B13 in complex with cofactor and inhibitor -

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Basic information

Entry
Database: PDB / ID: 8g89
TitleHSD17B13 in complex with cofactor and inhibitor
ComponentsHydroxysteroid 17-beta dehydrogenase 13
KeywordsOXIDOREDUCTASE/INHIBITOR / 17 beta-hydroxysteroid dehydrogenase 13 / lipid droplet associated protein / inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homologysteroid dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-YXW / Hydroxysteroid 17-beta dehydrogenase 13
Function and homology information
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.222 Å
AuthorsLiu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of lipid-droplet localization of 17-beta-hydroxysteroid dehydrogenase 13.
Authors: Liu, S. / Sommese, R.F. / Nedoma, N.L. / Stevens, L.M. / Dutra, J.K. / Zhang, L. / Edmonds, D.J. / Wang, Y. / Garnsey, M. / Clasquin, M.F.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)72,4475
Polymers70,7282
Non-polymers1,7183
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-46 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.03, 186.46, 65.47
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hydroxysteroid 17-beta dehydrogenase 13 / Hydroxysteroid 17-beta dehydrogenase 11


Mass: 35364.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSD17B13 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / 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-YXW / 3-fluoro-N-({(1r,4r)-4-[(2-fluorophenoxy)methyl]-1-hydroxycyclohexyl}methyl)-4-hydroxybenzamide


Mass: 391.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23F2NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG3350, 0.2 M ammonium chloride

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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: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→71.19 Å / Num. obs: 32599 / % possible obs: 92.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rpim(I) all: 0.039 / Net I/σ(I): 14.2
Reflection shellResolution: 2.23→2.47 Å / Num. unique obs: 1631 / CC1/2: 0.79 / Rpim(I) all: 0.57

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8G84

8g84


Resolution: 2.222→23.16 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.304 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1607 -RANDOM
Rwork0.2086 ---
obs0.2095 32551 68.8 %-
Displacement parametersBiso mean: 65.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.847 Å20 Å20 Å2
2--1.682 Å20 Å2
3----0.835 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.222→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 116 81 4750
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.916560HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1665SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes804HARMONIC5
X-RAY DIFFRACTIONt_it4777HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion658SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3691SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion19.46
LS refinement shellResolution: 2.222→2.39 Å
RfactorNum. reflection% reflection
Rfree0.2505 22 -
Rwork0.2856 --
obs--6.9 %
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)
11.65910.0956-0.44321.04770.1954.30070.01160.01430.68830.01430.03810.17260.68830.1726-0.0497-0.13050.0566-0.0422-0.2299-0.028-0.150834.803230.07161.1144
22.0267-0.5389-0.11591.2519-0.04683.8931-0.01530.09840.7010.09840.0237-0.54070.701-0.5407-0.0085-0.0928-0.1198-0.0093-0.13370.0191-0.146915.763829.779484.5116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 286
2X-RAY DIFFRACTION1{ A|* }A296 - 301
3X-RAY DIFFRACTION2{ B|* }B2 - 295
4X-RAY DIFFRACTION2{ B|* }B296

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