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- PDB-8orn: Crystal structure of Xanthomonas campestris pv. campestris LolA-L... -

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Basic information

Entry
Database: PDB / ID: 8orn
TitleCrystal structure of Xanthomonas campestris pv. campestris LolA-LolB complex
Components
  • Outer-membrane lipoprotein LolB
  • Outer-membrane lipoprotein carrier protein
KeywordsLIPID BINDING PROTEIN / Lipoprotein transport / Lol pathway / LolA / LolB / protein-protein complex / Xanthomonas campestris pv. campestris / plant pathogen
Function / homology
Function and homology information


lipoprotein localization to outer membrane / lipoprotein transport / cell outer membrane / protein transport / periplasmic space
Similarity search - Function
Outer membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Outer-membrane lipoprotein carrier protein / Outer-membrane lipoprotein LolB
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris str. B100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFurlanetto, V. / Divne, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research CouncilFORMAS 2017-00983 Sweden
Swedish Research CouncilOscar and Lili Lamm Memorial Foundation DO2017-0020 Sweden
CitationJournal: Front Microbiol / Year: 2023
Title: LolA and LolB from the plant-pathogen Xanthomonas campestris forms a stable heterodimeric complex in the absence of lipoprotein.
Authors: Furlanetto, V. / Divne, C.
History
DepositionApr 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer-membrane lipoprotein carrier protein
B: Outer-membrane lipoprotein LolB
C: Outer-membrane lipoprotein carrier protein
D: Outer-membrane lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9326
Polymers91,7404
Non-polymers1922
Water48627
1
A: Outer-membrane lipoprotein carrier protein
B: Outer-membrane lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9663
Polymers45,8702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-14 kcal/mol
Surface area17200 Å2
2
C: Outer-membrane lipoprotein carrier protein
D: Outer-membrane lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9663
Polymers45,8702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area17770 Å2
Unit cell
Length a, b, c (Å)137.510, 137.510, 145.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Outer-membrane lipoprotein carrier protein


Mass: 22694.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LolA is chain A and C LolB is chain B and D A and B form a complex C and D form a complex
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. B100 (bacteria)
Strain: B100 / Gene: lolA, xcc-b100_2273 / Plasmid: pNIC-CTHO / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: B0RT42
#2: Protein Outer-membrane lipoprotein LolB


Mass: 23175.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LolA is chain A and C LolB is chain B and D A and B form a complex C and D form a complex
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. B100 (bacteria)
Strain: B100 / Gene: lolB, xcc-b100_3479 / Plasmid: pNIC-CTHO / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: B0RUA2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.29 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM Hepes pH 7.5, 2.5 M (NH4)2SO4 and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2022 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)
RadiationMonochromator: Si(111) double crystal monochromator, horizontally deflecting
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.2→48.4 Å / Num. obs: 51938 / % possible obs: 99.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 66.42 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6459 / CC1/2: 0.492 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.4 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 34.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1995 3.84 %
Rwork0.2209 --
obs0.2225 51928 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 10 27 5703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085806
X-RAY DIFFRACTIONf_angle_d1.0157884
X-RAY DIFFRACTIONf_dihedral_angle_d6.212798
X-RAY DIFFRACTIONf_chiral_restr0.058835
X-RAY DIFFRACTIONf_plane_restr0.0111053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.5491400.54253534X-RAY DIFFRACTION100
2.26-2.320.45511420.46893570X-RAY DIFFRACTION100
2.32-2.380.43641460.38263588X-RAY DIFFRACTION100
2.38-2.460.34941430.31733570X-RAY DIFFRACTION100
2.46-2.550.31121410.30213554X-RAY DIFFRACTION100
2.55-2.650.32341400.28883585X-RAY DIFFRACTION100
2.65-2.770.34271370.31263551X-RAY DIFFRACTION100
2.77-2.920.31631440.28453591X-RAY DIFFRACTION100
2.92-3.10.30821410.26443547X-RAY DIFFRACTION100
3.1-3.340.30081430.23773571X-RAY DIFFRACTION100
3.34-3.680.23251450.22873573X-RAY DIFFRACTION100
3.68-4.210.25291400.18273582X-RAY DIFFRACTION100
4.21-5.290.18411460.16153545X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 54.1479 Å / Origin y: 16.3223 Å / Origin z: -17.8433 Å
111213212223313233
T0.4421 Å20.018 Å20.0059 Å2-0.4751 Å2-0.0216 Å2--0.4898 Å2
L0.5818 °20.2095 °20.1559 °2-0.5898 °2-0.0462 °2--0.5976 °2
S0.0506 Å °0.0048 Å °-0.0213 Å °0.0143 Å °0.0571 Å °0.0088 Å °-0.046 Å °0.0462 Å °0 Å °
Refinement TLS groupSelection details: all

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