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

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Basic information

Entry
Database: PDB / ID: 5ich
TitleCrystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8BO-AMP
ComponentsLipoate--protein ligase
KeywordsLIGASE / TRANSFERASE / PROTEIN-SUBSTRATE COMPLEX / LIPOATE ANALOG
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
Chem-SH5 / 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 8BO-AMP
Authors: Hughes, S.J. / Song, J.H. / Antoshchenko, T. / Park, H.W.
History
DepositionFeb 23, 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
B: Lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2064
Polymers81,1012
Non-polymers1,1052
Water9,872548
1
A: Lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1032
Polymers40,5511
Non-polymers5521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoate--protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1032
Polymers40,5511
Non-polymers5521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.917, 69.383, 97.664
Angle α, β, γ (deg.)90.000, 92.300, 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.: 2
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-SH5 / 5'-O-[(S)-[(8-bromooctanoyl)oxy](hydroxy)phosphoryl]adenosine


Mass: 552.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H27BrN5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.13 Å3/Da / Density % sol: 42.13 % / Mosaicity: 0.276 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 1.5 UL PROTEIN + 1.5 UL BUFFER (27% 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: 0.97905 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: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 58160 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.018 / Rrim(I) all: 0.041 / Χ2: 1.701 / Net I/av σ(I): 48.804 / Net I/σ(I): 23.7 / Num. measured all: 282553
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.924.10.12658220.9840.070.1451.599100
1.92-1.994.50.09757720.9920.050.111.688100
1.99-2.0850.08357900.9950.040.0921.912100
2.08-2.1950.06758040.9960.0330.0751.807100
2.19-2.3350.06158160.9970.030.0681.917100
2.33-2.515.10.04657840.9980.0220.0521.637100
2.51-2.765.10.0458190.9990.0190.0451.612100
2.76-3.165.10.03258590.9990.0160.0361.602100
3.16-3.9950.02658480.9990.0130.0291.52100
3.99-504.70.02658460.9990.0130.031.69698.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation22.2 Å2.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALEPACKdata scaling
MOLREP11.0.05phasing
PDB_EXTRACT3.2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBY

5iby


Resolution: 1.85→21.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2108 / WRfactor Rwork: 0.1747 / FOM work R set: 0.872 / SU B: 5.108 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1381 / SU Rfree: 0.1265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 2935 5.1 %RANDOM
Rwork0.1694 ---
obs0.1712 55147 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.88 Å2 / Biso mean: 23.297 Å2 / Biso min: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å20.03 Å2
2--1.1 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.85→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 66 548 5738
Biso mean--20.9 28.98 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195482
X-RAY DIFFRACTIONr_bond_other_d0.0010.025125
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9657430
X-RAY DIFFRACTIONr_angle_other_deg0.7223.00511811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71925.322295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01915964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0511527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021282
X-RAY DIFFRACTIONr_mcbond_it1.0290.8972618
X-RAY DIFFRACTIONr_mcbond_other1.0290.8972616
X-RAY DIFFRACTIONr_mcangle_it1.6621.3373290
LS refinement shellResolution: 1.85→1.914 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.258 282 -
Rwork0.209 5385 -
all-5667 -
obs--99.96 %
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)
12.52930.1969-0.11311.1754-0.36761.37140.1024-0.04690.01060.0713-0.1003-0.07040.03730.0537-0.00210.0237-0.00240.00560.01060.00620.0245-15.50330.313242.9166
24.10660.2961.43720.70080.04323.4683-0.0290.19490.1634-0.16770.04420.0725-0.1522-0.101-0.01520.06250.01380.01330.0670.01710.0773-37.36578.741425.3289
32.9683-0.30270.65651.19890.28362.51120.0687-0.08750.0206-0.05-0.02030.01140.1129-0.0374-0.04840.1106-0.01590.00540.0331-0.01220.0681-13.287635.0815.7723
44.8551-0.44080.14881.0931.02544.3548-0.0638-0.18050.1758-0.05960.1921-0.0471-0.1890.5464-0.12830.0928-0.0032-0.00970.1467-0.02580.08218.83444.469623.4016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 247
2X-RAY DIFFRACTION2A248 - 334
3X-RAY DIFFRACTION3B-2 - 247
4X-RAY DIFFRACTION4B248 - 334

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