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- PDB-8g9v: Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13 -

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Basic information

Entry
Database: PDB / ID: 8g9v
TitleCrystal structures of 17-beta-hydroxysteroid dehydrogenase 13
Components17-beta-hydroxysteroid dehydrogenase 13
KeywordsOXIDOREDUCTASE/INHIBITOR / 17 beta-hydroxysteroid dehydrogenase 13 / lipid droplet associated protein / inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


Lipid particle organization / all-trans-retinol dehydrogenase (NAD+) / steroid dehydrogenase activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / all-trans-retinol dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / positive regulation of lipid biosynthetic process / lipid droplet ...Lipid particle organization / all-trans-retinol dehydrogenase (NAD+) / steroid dehydrogenase activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / all-trans-retinol dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / positive regulation of lipid biosynthetic process / lipid droplet / lipid metabolic process / endoplasmic reticulum / cytosol
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
O-DODECANYL OCTAETHYLENE GLYCOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-YYC / 17-beta-hydroxysteroid dehydrogenase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 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 22, 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

Downloads & links

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Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 13
B: 17-beta-hydroxysteroid dehydrogenase 13
C: 17-beta-hydroxysteroid dehydrogenase 13
D: 17-beta-hydroxysteroid dehydrogenase 13
E: 17-beta-hydroxysteroid dehydrogenase 13
F: 17-beta-hydroxysteroid dehydrogenase 13
G: 17-beta-hydroxysteroid dehydrogenase 13
H: 17-beta-hydroxysteroid dehydrogenase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,79145
Polymers284,0198
Non-polymers12,77237
Water41423
1
A: 17-beta-hydroxysteroid dehydrogenase 13
B: 17-beta-hydroxysteroid dehydrogenase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,17411
Polymers71,0052
Non-polymers3,1699
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-137 kcal/mol
Surface area24200 Å2
MethodPISA
2
C: 17-beta-hydroxysteroid dehydrogenase 13
D: 17-beta-hydroxysteroid dehydrogenase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,71212
Polymers71,0052
Non-polymers3,70810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-110 kcal/mol
Surface area23470 Å2
MethodPISA
3
E: 17-beta-hydroxysteroid dehydrogenase 13
F: 17-beta-hydroxysteroid dehydrogenase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,17411
Polymers71,0052
Non-polymers3,1699
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-94 kcal/mol
Surface area25070 Å2
MethodPISA
4
G: 17-beta-hydroxysteroid dehydrogenase 13
H: 17-beta-hydroxysteroid dehydrogenase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,73111
Polymers71,0052
Non-polymers2,7269
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-111 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.150, 161.560, 100.770
Angle α, β, γ (deg.)90.00, 95.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
17-beta-hydroxysteroid dehydrogenase 13 / 17-beta-HSD 13 / Short chain dehydrogenase/reductase family 16C member 3 / Short-chain ...17-beta-HSD 13 / Short chain dehydrogenase/reductase family 16C member 3 / Short-chain dehydrogenase/reductase 9


Mass: 35502.348 Da / Num. of mol.: 8 / Mutation: Q60K, I62R, R71H, E161K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B13, SCDR9, SDR16C3, HMFN0376, UNQ497/PRO1014 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7Z5P4, Oxidoreductases; Acting on the CH-OH group of donors

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Non-polymers , 5 types, 60 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-YYC / 4-{[2,5-dimethyl-3-(4-methylbenzene-1-sulfonyl)benzene-1-sulfonyl]amino}benzoic acid


Mass: 459.535 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H21NO6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT


Mass: 538.755 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H58O9
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2M Li2SO4

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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: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.645→90.95 Å / Num. obs: 67940 / % possible obs: 93.4 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rpim(I) all: 0.083 / Net I/σ(I): 7.9
Reflection shellResolution: 2.645→2.897 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3398 / CC1/2: 0.462 / Rpim(I) all: 0.589

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.645→37.91 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 3399 5.01 %RANDOM
Rwork0.212 ---
obs0.2136 67909 76.1 %-
Displacement parametersBiso mean: 61.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.6003 Å20 Å21.2256 Å2
2---0.6366 Å20 Å2
3---1.2369 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.645→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17326 0 777 23 18126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00818718HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9825643HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6485SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3418HARMONIC5
X-RAY DIFFRACTIONt_it18450HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion20.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2495SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14320SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.8 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3382 -3.9 %
Rwork0.2909 1306 -
all0.2928 1359 -
obs--9.68 %
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)
10.31840.1021-0.23240.57320.17721.2035-0.0186-0.0123-0.0541-0.0178-0.004-0.01640.15580.1880.0226-0.02480.0770.0011-0.008-0.0135-0.027228.82733.36577.1931
20.1250.06840.12490.5779-0.26150.44860.0285-0.02620.07760.0493-0.02590.1627-0.01060.0783-0.00260.02270.00920.0247-0.0486-0.06620.021315.345222.150620.0943
30.8983-0.24750.16760.8108-0.31370.18440.14040.0888-0.1332-0.2018-0.05730.06490.06470.0505-0.08310.03610.0804-0.0813-0.0628-0.0475-0.0026-7.577722.0776-19.7755
41.7021-0.2037-0.24750.3574-0.0270.25580.0941-0.10150.0549-0.05820.04720.0318-0.0392-0.0543-0.1413-0.05210.02410.0015-0.05190.04820.0499-24.91238.1773-6.5466
50.749-0.05590.41260.0406-0.15870.44060.0350.29830.13370.0099-0.20290.00250.080.18270.1678-0.12460.02220.06190.05290.15450.039223.451661.2965-32.8956
60.8899-0.12620.47370.3983-0.38990.745-0.0021-0.00040.22340.0814-0.1035-0.10440.03150.00230.1056-0.0830.01670.0272-0.08450.02540.122326.441853.6557-5.2835
70.81070.45040.0160.01920.55321.93240.1533-0.09070.04680.1295-0.046-0.01990.38180.4166-0.10730.08710.0453-0.00630.0471-0.0223-0.167637.0617-5.7449-41.0106
80.64920.48320.1870.14420.50030.93180.1878-0.12890.20650.0691-0.31140.13520.3134-0.13870.12360.0848-0.14160.1015-0.027-0.1248-0.11319.1899-12.6256-44.1035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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