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- PDB-7tpm: Structure of the outer-membrane lipoprotein carrier protein (LolA... -

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Basic information

Entry
Database: PDB / ID: 7tpm
TitleStructure of the outer-membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi
ComponentsOuter membrane lipoprotein carrier protein LolA
KeywordsLIPID TRANSPORT / lipoprotein carrier protein / LolA / Borreliella burgdorferi / Lyme disease spirochete
Function / homologyOuter 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 / Mainly Beta / Export chaperone
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / Resolution: 1.9 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Zueckert, W.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: Structure of the outer-membrane lipoprotein carrier protein (LolA) from Borrelia burgdorferi
Authors: Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Zueckert, W.R.
History
DepositionJan 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,8876
Polymers23,4041
Non-polymers4845
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.136, 122.136, 122.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Outer membrane lipoprotein carrier protein LolA / Export chaperone


Mass: 23403.543 Da / Num. of mol.: 1 / Fragment: Q18-N216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: BB_0346 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O51321
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 62.08 % / Mosaicity: 0.04 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M sodium formate, 100 mM MES, 5% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.86 Å / Num. obs: 25182 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 33.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.5 / Num. measured all: 488064 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.9420.12.3913202215970.7381.5100
9.11-49.8615.10.06545022990.99735.199.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXdev_3111refinement
XDSdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
CRANK2phasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD-phased structure of the same protein from a KI-soaked crystal

Resolution: 1.9→38.623 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.06 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1274 5.07 %
Rwork0.1906 23850 -
obs0.1927 25124 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.69 Å2 / Biso mean: 37.2703 Å2 / Biso min: 20.3 Å2
Refinement stepCycle: final / Resolution: 1.9→38.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 26 158 1665
Biso mean--54.45 44.23 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011548
X-RAY DIFFRACTIONf_angle_d1.0282096
X-RAY DIFFRACTIONf_dihedral_angle_d12.774921
X-RAY DIFFRACTIONf_chiral_restr0.062236
X-RAY DIFFRACTIONf_plane_restr0.007268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.97610.32671320.26792593
1.9761-2.0660.29311300.23332585
2.066-2.1750.2471470.2082592
2.175-2.31120.2461260.20082625
2.3112-2.48960.26591430.20322614
2.4896-2.74010.25961490.20652629
2.7401-3.13650.24551540.20382647
3.1365-3.9510.21161410.16932694
3.951-38.6230.20281520.17722871

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