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- PDB-6fhm: Crystal structure of the F47E mutant of the lipoprotein localizat... -

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Basic information

Entry
Database: PDB / ID: 6fhm
TitleCrystal structure of the F47E mutant of the lipoprotein localization factor, LolA
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsPROTEIN TRANSPORT / Lipoprotein transport / domain-swapped dimer
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 / Outer-membrane lipoprotein carrier protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKaplan, E. / Greene, N.P. / Crow, A. / Koronakis, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000994/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Insights into bacterial lipoprotein trafficking from a structure of LolA bound to the LolC periplasmic domain.
Authors: Kaplan, E. / Greene, N.P. / Crow, A. / Koronakis, V.
History
DepositionJan 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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: Outer-membrane lipoprotein carrier protein
B: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1115
Polymers45,8342
Non-polymers2763
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-33 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.030, 77.600, 103.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 22917.148 Da / Num. of mol.: 2 / Mutation: F47E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lolA, lplA, yzzV, b0891, JW0874 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61316
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / Details: 13% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.39→62.11 Å / Num. obs: 20165 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.086 / Rrim(I) all: 0.215 / Net I/σ(I): 6.7
Reflection shellResolution: 2.39→2.48 Å / Rpim(I) all: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWL

1iwl


Resolution: 2.39→62.11 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.146 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.262 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1018 5.1 %RANDOM
Rwork0.21469 ---
obs0.21746 19110 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--4.71 Å2-0 Å2
3----3.93 Å2
Refinement stepCycle: 1 / Resolution: 2.39→62.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 18 48 3035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193070
X-RAY DIFFRACTIONr_bond_other_d0.0060.022666
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9214162
X-RAY DIFFRACTIONr_angle_other_deg1.00436235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75225.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30615503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2721513
X-RAY DIFFRACTIONr_chiral_restr0.10.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9756.0141520
X-RAY DIFFRACTIONr_mcbond_other4.9766.0111519
X-RAY DIFFRACTIONr_mcangle_it7.6299.0061900
X-RAY DIFFRACTIONr_mcangle_other7.6289.0091901
X-RAY DIFFRACTIONr_scbond_it5.2456.1351550
X-RAY DIFFRACTIONr_scbond_other5.2386.1361550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9459.0232263
X-RAY DIFFRACTIONr_long_range_B_refined10.91868.4023368
X-RAY DIFFRACTIONr_long_range_B_other10.91668.4013366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 80 -
Rwork0.349 1403 -
obs--100 %

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