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- PDB-9g95: Lipid III flippase WzxE with NB10 nanobody in outward-facing conf... -

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Basic information

Entry
Database: PDB / ID: 9g95
TitleLipid III flippase WzxE with NB10 nanobody in outward-facing conformation at 2.7552 A
Components
  • Lipid III flippase
  • NB10 Nanobody
KeywordsTRANSPORT PROTEIN / membrane protein / flippase / cell wall / enterobacterial common antigen / lipid III
Function / homology
Function and homology information


intramembrane lipid transporter activity / enterobacterial common antigen biosynthetic process / plasma membrane
Similarity search - Function
Polysaccharide biosynthesis protein / Lipid III flippase WzxE, Proteobacteria / Lipid III flippase WzxE / : / Polysaccharide biosynthesis protein
Similarity search - Domain/homology
Chem-MPG / N-OCTANE / Lipid III flippase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLe Bas, A. / El Omari, K. / Lee, M. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Open Biology / Year: 2025
Title: Structure of WzxE the lipid III flippase for Enterobacterial Common Antigen polysaccharide.
Authors: Le Bas, A. / Clarke, B.R. / Teelucksingh, T. / Lee, M. / El Omari, K. / Giltrap, A.M. / McMahon, S.A. / Liu, H. / Beale, J.H. / Mykhaylyk, V. / Duman, R. / Paterson, N.G. / Ward, P.N. / ...Authors: Le Bas, A. / Clarke, B.R. / Teelucksingh, T. / Lee, M. / El Omari, K. / Giltrap, A.M. / McMahon, S.A. / Liu, H. / Beale, J.H. / Mykhaylyk, V. / Duman, R. / Paterson, N.G. / Ward, P.N. / Harrison, P.J. / Weckener, M. / Pardon, E. / Steyaert, J. / Liu, H. / Quigley, A. / Davis, B.G. / Wagner, A. / Whitfield, C. / Naismith, J.H.
History
DepositionJul 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid III flippase
B: NB10 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94617
Polymers61,2632
Non-polymers2,68215
Water00
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)271.540, 38.450, 56.960
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Lipid III flippase


Mass: 46130.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wzxE, wzx, yifJ, b3792, JW3766 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0AAA7
#2: Antibody NB10 Nanobody


Mass: 15132.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): wk6(su-)

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Non-polymers , 5 types, 15 molecules

#3: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Details

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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Na acetate, PEG400, lithium sulfate, zinc chloride, E. coli polar lipids, monoolein
PH range: 6.4-6.43

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 2.8→45.19 Å / Num. obs: 14932 / % possible obs: 100 % / Redundancy: 85.1 % / CC1/2: 0.999 / Χ2: 0.91 / Net I/σ(I): 30.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2147 / CC1/2: 0.872 / Χ2: 0.73 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.78 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 704 4.72 %
Rwork0.2359 --
obs0.2383 14921 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 178 0 4310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024387
X-RAY DIFFRACTIONf_angle_d0.6585913
X-RAY DIFFRACTIONf_dihedral_angle_d16.4081569
X-RAY DIFFRACTIONf_chiral_restr0.037678
X-RAY DIFFRACTIONf_plane_restr0.004717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.36521600.28692773X-RAY DIFFRACTION100
3.02-3.320.31551500.27562787X-RAY DIFFRACTION100
3.32-3.80.2921370.24692858X-RAY DIFFRACTION100
3.8-4.790.24571220.22562852X-RAY DIFFRACTION100
4.79-44.780.29241350.21772947X-RAY DIFFRACTION100

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