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- PDB-8crj: Crystal structure of LplA1 in complex with lipoyl-AMP (Listeria m... -

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Basic information

Entry
Database: PDB / ID: 8crj
TitleCrystal structure of LplA1 in complex with lipoyl-AMP (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 / protein modification process / ATP binding
Similarity search - Function
Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / 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
Chem-LAQ / lipoate--protein ligase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _pdbx_initial_refinement_model.type / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,39819
Polymers38,4191
Non-polymers1,97918
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-92 kcal/mol
Surface area16220 Å2
Unit cell
Length a, b, c (Å)79.310, 79.310, 225.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein lipoate--protein ligase


Mass: 38419.449 Da / Num. of mol.: 1
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 , 6 types, 71 molecules

#2: Chemical ChemComp-LAQ / 5'-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE / LIPOYL-AMP


Mass: 535.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N5O8PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4.61 Å3/Da / Density % sol: 73.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 1.0 M LiCl, 20% PEG 6000

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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: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 22722 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2378

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8CRI

8cri


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 18.018 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 1135 5 %RANDOM
Rwork0.173 ---
obs0.1747 21558 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.08 Å2 / Biso mean: 74.053 Å2 / Biso min: 48.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.79 Å20 Å2
3---1.57 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 116 53 2879
Biso mean--106.24 68.34 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162715
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.6433866
X-RAY DIFFRACTIONr_angle_other_deg1.0421.5896253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22623.567157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14615506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6851515
X-RAY DIFFRACTIONr_chiral_restr0.040.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_rigid_bond_restr0.52935587
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 82 -
Rwork0.34 1549 -
all-1631 -
obs--98.85 %
Refinement TLS params.Method: refined / Origin x: 21.656 Å / Origin y: 46.147 Å / Origin z: 80.382 Å
111213212223313233
T0.0534 Å20.0118 Å20.0159 Å2-0.0825 Å2-0.012 Å2--0.0137 Å2
L0.2852 °2-0.0079 °20.0258 °2-0.3848 °20.1985 °2--0.604 °2
S0.0277 Å °-0.0413 Å °-0.0121 Å °0.0548 Å °-0.0104 Å °0.0086 Å °0.0258 Å °-0.0325 Å °-0.0173 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 331
2X-RAY DIFFRACTION1A401

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