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

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Basic information

Entry
Database: PDB / ID: 5idh
TitleCrystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8-bromooctanoic acid
ComponentsLipoate--protein ligase
KeywordsLIGASE / TRANSFERASE / Protein-ligand complex
Function / homology
Function and homology information


lipoate-protein ligase activity / lipoate-protein ligase / 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
8-bromooctanoic acid / lipoate--protein ligase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsHughes, S.J. / Song, J.H. / Antoshchenko, T. / Park, H.W.
CitationJournal: To Be Published
Title: Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8-bromooctanoic acid
Authors: Hughes, S.J. / Song, J.H. / Antoshchenko, T. / Park, H.W.
History
DepositionFeb 24, 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)40,7742
Polymers40,5511
Non-polymers2231
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.968, 67.757, 54.193
Angle α, β, γ (deg.)90.000, 115.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipoate--protein ligase


Mass: 40550.664 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-2, EF_2741 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q830N7, EC: 2.7.7.63
#2: Chemical ChemComp-SH6 / 8-bromooctanoic acid


Mass: 223.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15BrO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.04 Å3/Da / Density % sol: 39.65 % / Mosaicity: 0.317 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5 UL PROTEIN + 1.5 UL BUFFER (35% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.75)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 47386 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.044 / Net I/av σ(I): 37.968 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.55-1.584.10.3981100
1.58-1.614.10.3411100
1.61-1.644.10.3111100
1.64-1.674.20.2711100
1.67-1.714.20.2311100
1.71-1.754.20.2021100
1.75-1.794.20.1771100
1.79-1.844.20.1461100
1.84-1.894.20.1191100
1.89-1.954.20.0941100
1.95-2.024.20.0741100
2.02-2.14.20.061100
2.1-2.24.20.0571100
2.2-2.324.20.0581100
2.32-2.464.20.0611100
2.46-2.654.20.0521100
2.65-2.924.30.0431100
2.92-3.344.20.0331100
3.34-4.214.20.0271100
4.21-48.84.10.028198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.531
Highest resolutionLowest resolution
Rotation22.99 Å2 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALEPACKdata scaling
MOLREP11.1.03phasing
PDB_EXTRACT3.2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBY

5iby


Resolution: 1.55→48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.169 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2392 5.1 %RANDOM
Rwork0.1782 ---
obs0.1802 44806 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 96.84 Å2 / Biso mean: 24.408 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å20.19 Å2
2--0.49 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.55→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 22 314 2892
Biso mean--31.74 33.19 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192750
X-RAY DIFFRACTIONr_bond_other_d0.0010.022598
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9593721
X-RAY DIFFRACTIONr_angle_other_deg0.72235993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46725.274146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50415492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.021514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
X-RAY DIFFRACTIONr_mcbond_it2.1871.1991324
X-RAY DIFFRACTIONr_mcbond_other2.1811.21322
X-RAY DIFFRACTIONr_mcangle_it2.7891.7961669
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 197 -
Rwork0.224 3286 -
all-3483 -
obs--99.91 %
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)
12.63840.5510.13820.8472-0.0621.75760.0246-0.0173-0.2395-0.01020.0001-0.06160.2046-0.0423-0.02470.0493-0.00050.00380.00190.00310.02422.1812-0.386123.7376
24.28812.85681.26543.8961-1.01142.2422-0.22250.28810.3996-0.24690.2170.2672-0.0552-0.10660.00560.10720.09450.0270.18440.10260.1172-10.39434.670910.2766
35.406-1.4428-0.86881.83051.5161.29340.05850.43220.2697-0.2787-0.0395-0.0074-0.2581-0.0089-0.0190.06670.00670.0220.05380.05190.06557.33029.9179.2531
43.4723-0.6048-1.11461.39260.34322.4125-0.00370.033-0.0705-0.06440.03560.02890.05210.0722-0.03190.0367-0.0104-0.00350.0341-0.01370.008622.7248-7.59251.8245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 38
2X-RAY DIFFRACTION1A81 - 152
3X-RAY DIFFRACTION1A197 - 248
4X-RAY DIFFRACTION2A153 - 196
5X-RAY DIFFRACTION3A39 - 80
6X-RAY DIFFRACTION4A249 - 334

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