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- PDB-8chx: Structure and function of LolA from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 8chx
TitleStructure and function of LolA from Vibrio cholerae
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsLIPID TRANSPORT / Lipid / periplasm / gram-negative
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 / periplasmic space / Outer-membrane lipoprotein carrier protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJaiman, D. / Nagampalli, R. / Persson, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Swedish Research Council2007-08673 Sweden
CitationJournal: Sci Rep / Year: 2023
Title: A comparative analysis of lipoprotein transport proteins: LolA and LolB from Vibrio cholerae and LolA from Porphyromonas gingivalis.
Authors: Jaiman, D. / Nagampalli, R. / Persson, K.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)48,0379
Polymers47,5792
Non-polymers4587
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-132 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.485, 91.394, 48.459
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Outer-membrane lipoprotein carrier protein


Mass: 23789.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lolA, VC0395_A0626, VC395_1122 / Plasmid: petHis1a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5F2G9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES pH 5.0, 20 mM Zinc-acetate, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.8→45.83 Å / Num. obs: 37905 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Χ2: 1.07 / Net I/σ(I): 15.3 / Num. measured all: 375785
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.711 / Num. unique obs: 2234 / CC1/2: 0.871 / Rpim(I) all: 0.234 / Rrim(I) all: 0.749 / Χ2: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.8 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 1122 2.9 %random
Rwork0.2104 ---
obs-37474 99 %-
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 7 551 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632984
X-RAY DIFFRACTIONf_angle_d0.85574049
X-RAY DIFFRACTIONf_chiral_restr0.0561447
X-RAY DIFFRACTIONf_plane_restr0.0053537
X-RAY DIFFRACTIONf_dihedral_angle_d23.86261101

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