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- PDB-7z6w: Complex of E. coli LolA and lipoprotein -

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Basic information

Entry
Database: PDB / ID: 7z6w
TitleComplex of E. coli LolA and lipoprotein
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsTRANSPORT PROTEIN / Lipoprotein trafficking / PROTEIN TRANSPORT
Function / homologyOuter membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / lipoprotein transport / outer membrane-bounded periplasmic space / Chem-IG7 / Outer-membrane lipoprotein carrier protein
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKaplan, E. / Greene, N.P. / Koronakis, V.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N000994/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V000616/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural basis of lipoprotein recognition by the bacterial Lol trafficking chaperone LolA.
Authors: Kaplan, E. / Greene, N.P. / Jepson, A.E. / Koronakis, V.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4392
Polymers21,5301
Non-polymers9091
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10540 Å2
Unit cell
Length a, b, c (Å)90.980, 90.980, 47.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Outer-membrane lipoprotein carrier protein / P20


Mass: 21529.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lolA, lplA, yzzV, b0891, JW0874 / Production host: Escherichia coli (E. coli) / References: UniProt: P61316
#2: Chemical ChemComp-IG7 / [(2~{S})-3-[(2~{S})-3-azanyl-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate


Mass: 909.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H104N2O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.84→64.33 Å / Num. obs: 17042 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.037 / Rrim(I) all: 0.13 / Net I/σ(I): 14.3 / Num. measured all: 207055 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.8812.51.3741298110360.5360.4051.4332100
9.01-64.3312.70.029207916410.0080.0357.999.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UA8

1ua8


Resolution: 1.84→64.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.393 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 856 5 %RANDOM
Rwork0.1811 ---
obs0.1829 16184 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.33 Å2 / Biso mean: 29.02 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0 Å2
2--0.36 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.84→64.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 63 74 1629
Biso mean--48.4 35.99 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131589
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161381
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.6862137
X-RAY DIFFRACTIONr_angle_other_deg1.411.5953179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93424.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22615249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.161156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 79 -
Rwork0.288 1167 -
all-1246 -
obs--100 %

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