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- PDB-8g84: Crystal structures of HSD17B13 complexes -

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Basic information

Entry
Database: PDB / ID: 8g84
TitleCrystal structures of HSD17B13 complexes
ComponentsHydroxysteroid 17-beta dehydrogenase 13
KeywordsOXIDOREDUCTASE / 17 beta-hydroxysteroid dehydrogenase 13 / lipid droplet associated protein / inhibitor
Function / homology
Function and homology information


17beta-estradiol 17-dehydrogenase / lipid droplet / lipid metabolic process / oxidoreductase activity / nucleotide binding / endoplasmic reticulum
Similarity search - Function
short chain dehydrogenase / 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 / 17beta-estradiol 17-dehydrogenase
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.467 Å
AuthorsLiu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
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)72,0554
Polymers70,7282
Non-polymers1,3272
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-48 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.379, 187.205, 65.365
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 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.52 Å3/Da / Density % sol: 65.05 %
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 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.467→93.6 Å / Num. obs: 29109 / % possible obs: 93.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rpim(I) all: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 2.467→2.64 Å / Redundancy: 6.8 % / Num. unique obs: 1456 / CC1/2: 0.581 / Rpim(I) all: 0.579 / % possible all: 50.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.467→24.16 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.375 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.379 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1447 -RANDOM
Rwork0.1997 ---
obs0.2011 29060 84.1 %-
Displacement parametersBiso mean: 56.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.6476 Å20 Å20 Å2
2---0.0014 Å20 Å2
3----2.6462 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.467→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 88 136 4902
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074874HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.896636HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1686SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes800HARMONIC5
X-RAY DIFFRACTIONt_it4874HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion676SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3779SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion18.44
LS refinement shellResolution: 2.47→2.58 Å
RfactorNum. reflection% reflection
Rfree0.37 30 -
Rwork0.2647 --
obs0.2694 582 13.11 %
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)
10.6239-0.0676-0.07080.50380.05332.0615-0.05330.49090.32390.49090.10660.25340.32390.2534-0.05330.56720.1242-0.13080.65420.02640.03434.803230.07161.1144
20.5593-0.29650.34320.2737-0.08642.2728-0.3480.4250.29210.4250.3365-0.60560.2921-0.60560.01160.8670.36030.19491.17570.15070.157615.763829.779484.5116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|298 A|400 - A|400 }A2 - 298
2X-RAY DIFFRACTION1{ A|2 - A|298 A|400 - A|400 }A400
3X-RAY DIFFRACTION2{ B|2 - B|298 B|400 - B|400 }B2 - 298
4X-RAY DIFFRACTION2{ B|2 - B|298 B|400 - B|400 }B400

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