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- PDB-9oa3: N. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle -

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Basic information

Entry
Database: PDB / ID: 9oa3
TitleN. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle
ComponentsGalactofuranosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Membrane / Galactofuranose / Galactan / SMALP
Function / homologyGalactofuranosyltransferase GlfT2, N-terminal / Galactofuranosyltransferase-2, C-terminal / Galactofuranosyltransferase 2 N-terminal / Galactofuranosyltransferase-2, domain 3 / Glycosyltransferase like family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / Galactofuranosyltransferase
Function and homology information
Biological speciesNocardia brasiliensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsCarter, A.W. / Dodge, G.J. / Kiessling, L.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01 AI126592-09 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31 GM148069 United States
CitationJournal: To Be Published
Title: Structural Insights into Sequence-Controlled Polymerization by the Monotopic Glycosyltransferase GlfT2
Authors: Carter, A.W. / Dodge, G.J. / Keys, A.M. / Justen, A.M. / Taylor, K.I. / Imperiali, B. / Kulik, H.J. / Kiessling, L.L.
History
DepositionApr 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactofuranosyltransferase
B: Galactofuranosyltransferase
C: Galactofuranosyltransferase
D: Galactofuranosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,5138
Polymers295,4164
Non-polymers974
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 14 - 638 / Label seq-ID: 36 - 660

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.999999446415, 0.000553184861764, 0.000895073353244), (-0.000553562004064, -0.999999758096, -0.000421160648354), (0.000894840157027, -0.000421655893805, 0.999999510734)317.729178622, 318.15515875, -0.078623495549
2given(-0.00101560104338, -0.999999259042, 0.000671170753982), (0.999999484247, -0.00101559559684, 8.45576769292E-6), (-7.77412336508E-6, 0.00067117899551, 0.999999774729)318.028545823, 0.20284662829, -0.139266838324
3given(0.000213563407158, 0.999999965531, -0.000152734560548), (-0.999999962076, 0.000213589960941, 0.000173860585691), (0.000173893202267, 0.000152697424497, 0.999999973222)-0.00365828810465, 317.929257856, -0.0663019427054

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Components

#1: Protein
Galactofuranosyltransferase


Mass: 73853.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia brasiliensis (bacteria) / Gene: O3I_000690 / Plasmid: pAWC25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0EQQ2
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotetrameric Complex of Galactofuranosyltransferase 2
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.295 MDa / Experimental value: NO
Source (natural)Organism: Nocardia brasiliensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: DE3 / Plasmid: pAWC25
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
1100 mMHEPES1
2150 mMsodium chloride1
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 250 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.68 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
4cryoSPARC4.6.0CTF correction
7PHENIX1.21.2_5419model fitting
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.03D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1552517
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182122 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9DTP

9dtp


Accession code: 9DTP / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002119636
ELECTRON MICROSCOPYf_angle_d0.578726704
ELECTRON MICROSCOPYf_chiral_restr0.04132964
ELECTRON MICROSCOPYf_plane_restr0.00453464
ELECTRON MICROSCOPYf_dihedral_angle_d3.90882687
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints5.85218594456E-11
ens_1d_3CCELECTRON MICROSCOPYNCS constraints1.46417330725E-12
ens_1d_4CCELECTRON MICROSCOPYNCS constraints6.28404388318E-13

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