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

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Basic information

Entry
Database: PDB / ID: 5iby
TitleCrystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with lipoic acid
ComponentsLipoate--protein ligase
KeywordsLIGASE / TRANSFERASE / PROTEIN-SUBSTRATE COMPLEX
Function / homology
Function and homology information


lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein modification process / ATP binding / cytosol
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
LIPOIC ACID / lipoate--protein ligase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 lipoic acid
Authors: Hughes, S.J. / Song, J.H. / Antoshchenko, T. / Park, H.W.
History
DepositionFeb 22, 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)40,7572
Polymers40,5511
Non-polymers2061
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.977, 68.561, 54.154
Angle α, β, γ (deg.)90.000, 116.130, 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.1 Å3/Da / Density % sol: 41.3 % / Mosaicity: 0.444 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 1.5 UL PROTEIN + 1.5 UL BUFFER (25% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.25)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979054 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2014
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979054 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 28555 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.018 / Rrim(I) all: 0.04 / Χ2: 1.436 / Net I/av σ(I): 45.352 / Net I/σ(I): 19.8 / Num. measured all: 139224
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.8840.16114110.9720.0910.1861.27799.2
1.88-1.924.10.16314340.9760.090.1871.70499.3
1.92-1.954.40.14214070.9810.0760.1621.60199.1
1.95-1.994.70.11614090.990.0590.1311.52699.5
1.99-2.045.10.10414220.9910.0510.1161.5699.6
2.04-2.0850.09914490.9920.0480.111.83699.6
2.08-2.145.10.08214050.9950.0390.0911.6299.7
2.14-2.1950.07614070.9950.0370.0851.55599.7
2.19-2.2650.08114440.9930.040.091.98199.8
2.26-2.335.10.06114120.9970.030.0681.51299.8
2.33-2.415.10.05214380.9980.0250.0581.39999.9
2.41-2.515.10.0514300.9980.0240.0551.38899.9
2.51-2.635.10.04514250.9980.0220.051.33599.9
2.63-2.765.10.03914290.9990.0190.0431.31699.9
2.76-2.945.10.03314390.9990.0160.0371.212100
2.94-3.165.10.02914440.9990.0140.0321.162100
3.16-3.485.10.02514370.9990.0120.0281.148100
3.48-3.9950.02214570.9990.010.0241.065100
3.99-5.024.90.0214360.9990.010.0220.91799.9
5.02-504.60.03214200.9980.0160.0361.68995.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.42
Highest resolutionLowest resolution
Rotation21.58 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: 1VQZ

1vqz


Resolution: 1.85→21.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2139 / WRfactor Rwork: 0.1663 / FOM work R set: 0.8639 / SU B: 5.881 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1369 / SU Rfree: 0.1314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1443 5.1 %RANDOM
Rwork0.1641 ---
obs0.1664 27075 99.4 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.31 Å2 / Biso mean: 26.679 Å2 / Biso min: 10.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.25 Å2
2--2.17 Å20 Å2
3----1.23 Å2
Refinement stepCycle: final / Resolution: 1.85→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 12 279 2890
Biso mean--19.67 32.63 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192754
X-RAY DIFFRACTIONr_bond_other_d0.0020.022584
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9553730
X-RAY DIFFRACTIONr_angle_other_deg0.69535952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9925.235149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50915488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4721514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
X-RAY DIFFRACTIONr_mcbond_it1.4091.2021326
X-RAY DIFFRACTIONr_mcbond_other1.4031.2021324
X-RAY DIFFRACTIONr_mcangle_it2.0651.7961668
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 96 -
Rwork0.221 1977 -
all-2073 -
obs--98.95 %
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)
13.06940.1328-0.7781.1530.36232.54820.11830.234-0.0255-0.018-0.12180.0511-0.1112-0.20270.00350.03050.019-0.0170.0382-0.00880.0187-24.34781.862718.9117
23.8419-0.17-1.38731.89970.42194.126-0.18970.0412-0.1485-0.03050.18730.10790.15690.40280.00240.0549-0.003-0.00210.0632-0.00620.0532-2.368-6.86861.3835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 247
2X-RAY DIFFRACTION2A248 - 334

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