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- PDB-8cri: Crystal structure of LplA1 in complex with lipoic acid (Listeria ... -

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Basic information

Entry
Database: PDB / ID: 8cri
TitleCrystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)
Componentslipoate--protein ligase
KeywordsLIGASE / LIPOATE / SALVAGE / ANTI-INFECTIVES / DRUG DEVELOPMENT
Function / homology
Function and homology information


lipoate-protein ligase / lipoate-protein ligase activity / ATP binding / metal ion binding
Similarity search - Function
Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / Lipoyl protein ligase A/B catalytic domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
LIPOIC ACID / lipoate--protein ligase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDienemann, J.-N. / Chen, S.-Y. / Hitzenberger, M. / Sievert, M.L. / Hacker, S.M. / Prigge, S.T. / Zacharias, M. / Groll, M. / Sieber, S.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites.
Authors: Dienemann, J.N. / Chen, S.Y. / Hitzenberger, M. / Sievert, M.L. / Hacker, S.M. / Prigge, S.T. / Zacharias, M. / Groll, M. / Sieber, S.A.
History
DepositionMar 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lipoate--protein ligase
B: lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2396
Polymers76,8392
Non-polymers4004
Water1,802100
1
A: lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8195
Polymers38,4191
Non-polymers4004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lipoate--protein ligase


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.870, 72.790, 93.050
Angle α, β, γ (deg.)90.00, 98.04, 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 lipoate--protein ligase


Mass: 38419.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF817_03905, AF817_17765, APD94_04200, APD94_16795, D4271_05835, D4271_17085, D4C60_07100, D4C60_17245, D4D89_06525, D4D89_17125, D4U23_01750, D4U23_16900, E0I39_06590, E0I39_16500, E1V33_ ...Gene: AF817_03905, AF817_17765, APD94_04200, APD94_16795, D4271_05835, D4271_17085, D4C60_07100, D4C60_17245, D4D89_06525, D4D89_17125, D4U23_01750, D4U23_16900, E0I39_06590, E0I39_16500, E1V33_06915, E1W43_02450, E1W43_16025, FJU19_06430, FJU19_16220, FORC68_0962, G3R95_001339, G3R95_003435, GON91_05790, GT011_03885, GT011_16715, GXB45_04655, GXB45_16710, GYP27_11270, GYP27_15895, GYU24_04270, GYU24_17075
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D2IX29, lipoate-protein ligase

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Non-polymers , 5 types, 104 molecules

#2: Chemical ChemComp-LPA / LIPOIC ACID / 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid


Mass: 206.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM NH4Cl, 2.2 M (NH4)2SO4 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 44270 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5813 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.188 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25145 2213 5 %RANDOM
Rwork0.22334 ---
obs0.22487 42047 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å2-6.14 Å2
2---1.41 Å20 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 22 100 4832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134813
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164615
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.6396497
X-RAY DIFFRACTIONr_angle_other_deg1.0461.58810609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07223.81273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76515863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6341524
X-RAY DIFFRACTIONr_chiral_restr0.0360.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.154.6712313
X-RAY DIFFRACTIONr_mcbond_other1.154.6712312
X-RAY DIFFRACTIONr_mcangle_it1.6486.992879
X-RAY DIFFRACTIONr_mcangle_other1.6476.992880
X-RAY DIFFRACTIONr_scbond_it0.9434.852500
X-RAY DIFFRACTIONr_scbond_other0.9434.8512501
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3487.2063619
X-RAY DIFFRACTIONr_long_range_B_refined2.61853.2245125
X-RAY DIFFRACTIONr_long_range_B_other2.56153.185113
X-RAY DIFFRACTIONr_rigid_bond_restr0.51439428
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 163 -
Rwork0.311 3101 -
obs--98.94 %
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)
10.03050.01060.00460.17550.08630.05560.0010.0010.0040.0028-0.00760.01120.0024-0.00340.00660.01430.00060.01920.03040.00110.026318.6586-15.16382.1405
20.0519-0.10680.07890.2412-0.21050.24280.010.0030.0001-0.0175-0.0130.0060.02340.02960.0030.0173-0.00070.01810.0369-0.00010.02182.0284-19.050639.1932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 901
2X-RAY DIFFRACTION2B3 - 331

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