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- PDB-5ij6: Crystal structure of Enterococcus faecalis lipoate-protein ligase... -

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Basic information

Entry
Database: PDB / ID: 5ij6
TitleCrystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-1) in complex with lipoic acid
ComponentsLipoate--protein ligase
KeywordsLIGASE / TRANSFERASE / PROTEIN-SUBSTRATE COMPLEX / LIPOIC ACID
Function / homology
Function and homology information


lipoate-protein ligase / protein lipoylation / ligase activity / 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
Similarity search - Domain/homology
LIPOIC ACID / Lipoate--protein ligase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHughes, S.J. / Lyle, A.G. / Song, J.H. / Antoshchenko, T. / Park, H.
CitationJournal: to be published
Title: Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-1) in complex with lipoic acid
Authors: Hughes, S.J. / Lyle, A.G. / Antoshchenko, T. / Park, H.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1194
Polymers40,7811
Non-polymers3383
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.011, 70.912, 106.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipoate--protein ligase


Mass: 40781.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: lplA-1, EF_0650 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q838C1, EC: 2.7.7.63
#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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.87 % / Mosaicity: 0.33 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 UL PROTEIN + 0.5 UL BUFFER (30% PEG 4K, 0.2 M LITHIUM SULFATE, 0.1 M Tris HCl, PH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 1, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→39.44 Å / Num. obs: 27879 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.052 / Rrim(I) all: 0.154 / Net I/σ(I): 9.1 / Num. measured all: 240100 / Scaling rejects: 44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.058.90.5931915021450.9180.2080.6293.3100
8.72-39.447.30.07129243990.990.0270.0761699.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å37.49 Å
Translation2.1 Å37.49 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBY

5iby


Resolution: 2→39.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2121 / WRfactor Rwork: 0.1832 / FOM work R set: 0.8701 / SU B: 7.152 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1571 / SU Rfree: 0.1382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1414 5.1 %RANDOM
Rwork0.1778 ---
obs0.1793 26261 99.33 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 113.98 Å2 / Biso mean: 33.667 Å2 / Biso min: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0 Å2
2--1.36 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 18 178 2798
Biso mean--35.42 35.27 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192684
X-RAY DIFFRACTIONr_bond_other_d0.0020.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.973620
X-RAY DIFFRACTIONr_angle_other_deg0.70735916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0285324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5224.627134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62715486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6971515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
LS refinement shellResolution: 2→2.108 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.279 184 -
Rwork0.204 3804 -
all-3988 -
obs--99.45 %
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)
11.7357-0.55370.03143.3858-0.59881.694-0.09640.02030.01470.13050.003-0.30810.06110.16970.09340.0913-0.0188-0.00740.0840.02370.04966.976771.0813133.9644
23.6574-1.1253-0.44212.7678-1.05412.0496-0.01840.00470.0479-0.02540.0375-0.0096-0.0459-0.0709-0.01910.0054-0.013-0.00310.12250.01440.01360.579888.0635110.6421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 247
2X-RAY DIFFRACTION2A248 - 337

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