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- PDB-9g9o: Lipid III flippase WzxE with NB10 and NB7 nanobodies in outward-f... -

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Basic information

Entry
Database: PDB / ID: 9g9o
TitleLipid III flippase WzxE with NB10 and NB7 nanobodies in outward-facing conformation - crystal 2
Components
  • Lipid III flippase
  • NB10 Nanobody
  • NB7 Nanobody
KeywordsTRANSPORT PROTEIN / membrane protein / flippase / cell wall / enterobacterial common antigen
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: 2.69 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)42.335, 154.019, 288.085
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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: sodium citrate, lithium sulfate, sodium chloride, PEG300, 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: 0.6702 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6702 Å / Relative weight: 1
ReflectionResolution: 2.69→39.27 Å / Num. obs: 26959 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Net I/σ(I): 4.1
Reflection shellResolution: 2.69→2.73 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1293 / CC1/2: 0.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→38.5 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3378 1295 4.83 %
Rwork0.2793 --
obs0.2822 26804 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 0 0 5104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025221
X-RAY DIFFRACTIONf_angle_d0.4517098
X-RAY DIFFRACTIONf_dihedral_angle_d3.755734
X-RAY DIFFRACTIONf_chiral_restr0.035811
X-RAY DIFFRACTIONf_plane_restr0.004881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.80.38831290.38012739X-RAY DIFFRACTION98
2.8-2.920.4131290.35612784X-RAY DIFFRACTION100
2.92-3.080.39361590.34072813X-RAY DIFFRACTION100
3.08-3.270.35011200.31532845X-RAY DIFFRACTION100
3.27-3.520.37471410.29162830X-RAY DIFFRACTION100
3.52-3.880.31341620.25152813X-RAY DIFFRACTION100
3.88-4.440.32921340.27772838X-RAY DIFFRACTION99
4.44-5.590.39421450.27452835X-RAY DIFFRACTION98
5.59-38.50.26151760.2283012X-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)
10.9364-0.16420.18050.77-0.16530.9206-0.1087-0.0596-0.0950.08530.12450.07-0.1149-0.0741-0.01530.36340.00130.03150.29380.01290.3998-4.6211-34.6703-46.4057
24.2843-1.3184-2.58134.13012.44635.531-0.03530.1339-0.0369-0.28540.1137-0.08820.31230.2168-0.12140.56420.0055-0.07050.3530.00270.3358-7.146-5.9632-13.0028
32.26130.22610.89592.7678-0.2356.4389-0.0125-0.27840.28390.75490.23350.1762-0.242-0.0953-0.19420.58570.06230.00220.309-0.00420.48315.1049-53.613-6.0493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 414)A1 - 414
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 127)B2 - 127
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 124)C2 - 124

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