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- PDB-8cm1: Lol B - Localization of lipoprotein B from Vibrio cholera -

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Basic information

Entry
Database: PDB / ID: 8cm1
TitleLol B - Localization of lipoprotein B from Vibrio cholera
ComponentsOuter-membrane lipoprotein LolB
KeywordsPROTEIN TRANSPORT / Localization of Lipoproteins
Function / homologyOuter membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / cell outer membrane / protein transport / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer-membrane lipoprotein LolB
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsJaiman, D. / 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 17, 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 LolB


Theoretical massNumber of molelcules
Total (without water)24,8281
Polymers24,8281
Non-polymers00
Water3,459192
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 area10030 Å2
Unit cell
Length a, b, c (Å)113.414, 113.414, 34.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Outer-membrane lipoprotein LolB


Mass: 24827.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: lolB, D6U24_00025, ERS013165_00010, ERS013207_00996 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H5XM84
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.55 Å3/Da / Density meas: 0.99 Mg/m3 / Density % sol: 51.77 % / Description: Needles and Rod
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M KCl, 0.1 M Bis-Tris 6.0, 18% w/v PEG4000 / PH range: 5.7-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.46→40.1 Å / Num. obs: 39405 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.026 / Rrim(I) all: 0.132 / Χ2: 0.98 / Net I/σ(I): 19.6
Reflection shellResolution: 1.46→1.512 Å / Rmerge(I) obs: 0.3738 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 3862 / CC1/2: 0.752 / CC star: 0.927 / Rpim(I) all: 0.3738 / Rrim(I) all: 0.5287 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
autoPROC1.20.1-4487data reduction
autoPROC1.20.1-4487data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→35.86 Å / SU ML: 0.1601 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1972 1932 4.91 %
Rwork0.1658 37410 -
obs0.1673 39342 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.12 Å2
Refinement stepCycle: LAST / Resolution: 1.46→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 0 192 1678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641584
X-RAY DIFFRACTIONf_angle_d0.95462176
X-RAY DIFFRACTIONf_chiral_restr0.0885240
X-RAY DIFFRACTIONf_plane_restr0.0067286
X-RAY DIFFRACTIONf_dihedral_angle_d5.8729210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.30821180.27822656X-RAY DIFFRACTION99.96
1.5-1.540.29391190.2432626X-RAY DIFFRACTION100
1.54-1.580.25091600.18612603X-RAY DIFFRACTION100
1.58-1.630.20951520.15982616X-RAY DIFFRACTION100
1.63-1.690.19671310.15292649X-RAY DIFFRACTION100
1.69-1.760.20311320.15222615X-RAY DIFFRACTION100
1.76-1.840.23951360.16272646X-RAY DIFFRACTION100
1.84-1.940.19121290.14522668X-RAY DIFFRACTION100
1.94-2.060.16931350.14192649X-RAY DIFFRACTION100
2.06-2.220.17861420.14292666X-RAY DIFFRACTION99.96
2.22-2.440.20511580.15632687X-RAY DIFFRACTION100
2.44-2.790.2161390.17182675X-RAY DIFFRACTION100
2.79-3.520.17691420.16922748X-RAY DIFFRACTION100
3.52-35.860.18841390.17062906X-RAY DIFFRACTION99.93

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