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- PDB-9g97: Lipid III flippase WzxE with NB10 nanobody in outward-facing conf... -

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Basic information

Entry
Database: PDB / ID: 9g97
TitleLipid III flippase WzxE with NB10 nanobody in outward-facing conformation at 0.9688 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-LOP / Chem-MPG / N-OCTANE / Lipid III flippase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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)65,35621
Polymers61,2632
Non-polymers4,09319
Water81145
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)270.550, 38.470, 56.830
Angle α, β, γ (deg.)90.00, 93.50, 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 , 7 types, 64 molecules

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


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-OCT / N-OCTANE


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.43
Details: sodium acetate, PEG400, lithium sulfate, zinc chloride, 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: 0.9688 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.31→135.02 Å / Num. obs: 25893 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 7.8
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1276 / CC1/2: 0.4 / % possible all: 98.2

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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: 2.31→51.19 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 1311 5.07 %
Rwork0.2141 --
obs0.2165 25882 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→51.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 274 45 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.584
X-RAY DIFFRACTIONf_dihedral_angle_d11.731787
X-RAY DIFFRACTIONf_chiral_restr0.039682
X-RAY DIFFRACTIONf_plane_restr0.004716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.40.34621270.27592728X-RAY DIFFRACTION98
2.4-2.510.28951130.25952683X-RAY DIFFRACTION98
2.51-2.640.3131370.24782706X-RAY DIFFRACTION99
2.64-2.810.3081670.22932671X-RAY DIFFRACTION99
2.81-3.030.25231610.22812698X-RAY DIFFRACTION99
3.03-3.330.2741630.21832702X-RAY DIFFRACTION99
3.33-3.810.26991550.20592767X-RAY DIFFRACTION99
3.81-4.80.2661430.18872768X-RAY DIFFRACTION99
4.8-51.190.20161450.20772848X-RAY DIFFRACTION99
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)
11.5143-0.34270.13490.88280.02890.9357-0.0040.14930.0583-0.0541-0.0425-0.0288-0.08920.15490.03580.2402-0.0076-0.04740.26910.00940.306690.185510.6618-2.7416
21.70060.27850.12892.196-0.45041.5839-0.02790.03290.0520.1904-0.0644-0.2618-0.05060.14830.08110.33440.0094-0.04680.2673-0.01630.324492.631618.213320.2917
32.04911.162-1.17712.33860.73911.86110.0263-0.5592-0.3191-0.081-0.0998-0.41860.05420.37180.07270.30950.10840.05640.77650.10980.6941125.2023.3694-18.6788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 232 )
2X-RAY DIFFRACTION2chain 'A' and (resid 233 through 418 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 127 )

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