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- PDB-8cgm: Structure of the lipoprotein transporter LolA from Porphyromonas ... -

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Basic information

Entry
Database: PDB / ID: 8cgm
TitleStructure of the lipoprotein transporter LolA from Porphyromonas gingivalis
ComponentsOuter membrane lipoprotein carrier protein LolA
KeywordsPROTEIN TRANSPORT / lipoprotein / transport / periplasm
Function / homologyOuter membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / FORMIC ACID / Outer membrane lipoprotein carrier protein LolA
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsPersson, K. / Jaiman, D. / Nagampalli, R.
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 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane lipoprotein carrier protein LolA
B: Outer membrane lipoprotein carrier protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4837
Polymers47,9082
Non-polymers5755
Water7,782432
1
A: Outer membrane lipoprotein carrier protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2413
Polymers23,9541
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane lipoprotein carrier protein LolA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2414
Polymers23,9541
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.810, 76.463, 99.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Outer membrane lipoprotein carrier protein LolA


Mass: 23954.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PG_1635 / Plasmid: pETHisA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MUA1
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Na formate, 0.2 M NH4acetate, 0.2 M Na citrate tribasic, 0.2 M Na/K tartrate, 0.1 M imidazole/MES pH 6.5, 40% PEG500mme, 20% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→49.72 Å / Num. obs: 41710 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.038 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 26.9 % / Rmerge(I) obs: 1.299 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4084 / CC1/2: 0.865 / Rpim(I) all: 0.359 / Rrim(I) all: 1.349 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→49.72 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1382 3.31 %random
Rwork0.1884 ---
obs0.1895 41699 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 36 432 3330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142970
X-RAY DIFFRACTIONf_angle_d1.5594014
X-RAY DIFFRACTIONf_dihedral_angle_d14.053434
X-RAY DIFFRACTIONf_chiral_restr0.063466
X-RAY DIFFRACTIONf_plane_restr0.007518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.33711350.28143948X-RAY DIFFRACTION100
1.76-1.830.30861360.24913965X-RAY DIFFRACTION100
1.83-1.910.24041360.21924002X-RAY DIFFRACTION100
1.91-2.020.23071370.20173988X-RAY DIFFRACTION100
2.02-2.140.22571370.18553990X-RAY DIFFRACTION100
2.14-2.310.2221380.19044004X-RAY DIFFRACTION100
2.31-2.540.22441370.18494022X-RAY DIFFRACTION100
2.54-2.910.23871400.19394047X-RAY DIFFRACTION100
2.91-3.660.19921400.17334086X-RAY DIFFRACTION100
3.66-49.720.20161460.17414265X-RAY DIFFRACTION100

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