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- PDB-9g9n: Lipid III flippase WzxE with NB10 and NB7 nanobodies in inward-fa... -

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Basic information

Entry
Database: PDB / ID: 9g9n
TitleLipid III flippase WzxE with NB10 and NB7 nanobodies in inward-facing conformation - crystal 1
Components
  • Lipid III flippase
  • NB10 Nanobody
  • NB7 Nanobody
KeywordsTRANSPORT PROTEIN / membrane protein / flippase / cell wall / enterobacterial common antigen / lipid III
Function / homologyintramembrane lipid transporter activity / Polysaccharide biosynthesis protein / Lipid III flippase WzxE, Proteobacteria / Lipid III flippase WzxE / : / Polysaccharide biosynthesis protein / enterobacterial common antigen biosynthetic process / plasma membrane / Lipid III flippase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLe Bas, A. / 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 25, 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
C: NB7 Nanobody


Theoretical massNumber of molelcules
Total (without water)76,4873
Polymers76,4873
Non-polymers00
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)84.240, 191.910, 101.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#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-
#3: Antibody NB7 Nanobody


Mass: 15223.880 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-
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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: tri-sodium citrate, lithium sulphate, sodium chloride, PEG400, E coli polar lipids, monoolein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.8→33.8 Å / Num. obs: 20612 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 6.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1002 / CC1/2: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→32.4 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3133 1027 4.99 %
Rwork0.2558 --
obs0.2587 20563 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5060 0 0 0 5060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025177
X-RAY DIFFRACTIONf_angle_d0.4957037
X-RAY DIFFRACTIONf_dihedral_angle_d3.942726
X-RAY DIFFRACTIONf_chiral_restr0.037803
X-RAY DIFFRACTIONf_plane_restr0.004872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.43981350.36292736X-RAY DIFFRACTION100
2.95-3.130.42841640.33772751X-RAY DIFFRACTION100
3.13-3.370.37821390.30332783X-RAY DIFFRACTION100
3.37-3.710.32471460.26152758X-RAY DIFFRACTION100
3.71-4.250.26981400.23042803X-RAY DIFFRACTION100
4.25-5.350.32141390.23772791X-RAY DIFFRACTION99
5.35-32.40.24671640.21942914X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71110.206-0.09380.4547-0.59090.78680.048-0.02470.14350.2366-0.0338-0.0154-0.11530.07660.00880.8002-0.0380.06320.2863-0.02480.397720.44692.038724.9379
23.8782-2.7161-0.78665.38232.64761.6242-0.12230.0982-0.2656-0.3270.00630.01290.4123-0.11770.08980.9860.02470.06770.33870.02740.380118.0834-34.373410.8502
33.10751.56961.44456.0771-0.56020.98730.02450.0638-0.23060.3094-0.03-0.08150.52010.2615-0.01451.2450.1704-0.01560.44450.03980.360424.4295-39.505139.1763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 416)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 127)
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 124)

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