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- PDB-8tsk: Structure of human LIAS in the presence of 5'-deoxyadenosine and ... -

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Basic information

Entry
Database: PDB / ID: 8tsk
TitleStructure of human LIAS in the presence of 5'-deoxyadenosine and octanoyl-modified peptide
ComponentsLipoyl synthase, mitochondrial
KeywordsBIOSYNTHETIC PROTEIN / Lipoyl synthase / LIAS
Function / homology
Function and homology information


lipoyl synthase / lipoate synthase activity / lipoate biosynthetic process / Protein lipoylation / neural tube closure / 4 iron, 4 sulfur cluster binding / response to oxidative stress / response to lipopolysaccharide / mitochondrial matrix / inflammatory response ...lipoyl synthase / lipoate synthase activity / lipoate biosynthetic process / Protein lipoylation / neural tube closure / 4 iron, 4 sulfur cluster binding / response to oxidative stress / response to lipopolysaccharide / mitochondrial matrix / inflammatory response / mitochondrion / metal ion binding
Similarity search - Function
Lipoyl synthase, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / Lipoyl synthase / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
5'-DEOXYADENOSINE / LYSINE / METHIONINE / OCTANOIC ACID (CAPRYLIC ACID) / IRON/SULFUR CLUSTER / Lipoyl synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsEsakova, O.A. / Warui, D.M. / Neti, S.S. / Alumasa, J.N. / Booker, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-122595 United States
National Science Foundation (NSF, United States)MCB1716686 United States
Howard Hughes Medical Institute (HHMI)SJB United States
CitationJournal: To Be Published
Title: Structural basis for the mechanism of the human lipoyl synthase (LIAS) and its complex with the H-protein
Authors: Esakova, O.A. / Warui, D.M. / Neti, S.S. / Alumasa, J.N. / Booker, S.J.
History
DepositionAug 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoyl synthase, mitochondrial
B: Lipoyl synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,27911
Polymers83,0312
Non-polymers2,2489
Water11,169620
1
A: Lipoyl synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3684
Polymers41,5161
Non-polymers8523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoyl synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9117
Polymers41,5161
Non-polymers1,3956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.536, 69.025, 93.790
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipoyl synthase, mitochondrial


Mass: 41515.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIAS / Production host: Escherichia (bacteria) / References: UniProt: O43766

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Non-polymers , 6 types, 629 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.2 M sodium sulfate, 30% (w/v) PEG 3350, 3% (w/v) D-(+)-trehalose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 586767 / % possible obs: 98.6 % / Redundancy: 7 % / CC1/2: 0.995 / Net I/σ(I): 20.5
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 3623 / CC1/2: 0.653 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→27.77 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 3156 2.78 %
Rwork0.1778 --
obs0.1788 113483 68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 52 620 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064796
X-RAY DIFFRACTIONf_angle_d0.7696533
X-RAY DIFFRACTIONf_dihedral_angle_d13.6361812
X-RAY DIFFRACTIONf_chiral_restr0.073733
X-RAY DIFFRACTIONf_plane_restr0.006828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.3153320.27241105X-RAY DIFFRACTION20
1.6-1.630.3276360.24791449X-RAY DIFFRACTION20
1.63-1.650.25530.24081742X-RAY DIFFRACTION25
1.65-1.680.2684560.24792078X-RAY DIFFRACTION29
1.68-1.710.2847710.23352254X-RAY DIFFRACTION32
1.71-1.750.2464770.23672605X-RAY DIFFRACTION37
1.75-1.780.2257860.22962836X-RAY DIFFRACTION41
1.78-1.820.2391850.21743319X-RAY DIFFRACTION47
1.82-1.860.20171190.20553807X-RAY DIFFRACTION54
1.86-1.910.22651340.19394298X-RAY DIFFRACTION61
1.91-1.960.20891210.19534820X-RAY DIFFRACTION68
1.96-2.020.24991540.18795278X-RAY DIFFRACTION75
2.02-2.080.20941560.18275722X-RAY DIFFRACTION81
2.08-2.160.22271900.17826256X-RAY DIFFRACTION89
2.16-2.240.18321840.17526597X-RAY DIFFRACTION94
2.24-2.350.22891940.17826897X-RAY DIFFRACTION97
2.35-2.470.20862090.18087021X-RAY DIFFRACTION100
2.47-2.620.2421920.18717060X-RAY DIFFRACTION100
2.62-2.830.21562110.18697062X-RAY DIFFRACTION100
2.83-3.110.21811830.18187033X-RAY DIFFRACTION100
3.11-3.560.20672120.16497027X-RAY DIFFRACTION100
3.56-4.480.18392030.15227070X-RAY DIFFRACTION100
4.48-27.770.18861980.16076991X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -5.8901 Å / Origin y: 2.136 Å / Origin z: -26.0227 Å
111213212223313233
T0.076 Å20.0012 Å20.0071 Å2-0.0962 Å2-0.0356 Å2--0.0939 Å2
L0.5066 °2-0.0914 °20.1467 °2-1.3232 °2-0.8752 °2--1.1118 °2
S0.027 Å °0.0203 Å °-0.0325 Å °0.0674 Å °-0.0525 Å °-0.0313 Å °0.0582 Å °0.0952 Å °0.0222 Å °
Refinement TLS groupSelection details: all

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