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- PDB-5yys: Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (... -

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Basic information

Entry
Database: PDB / ID: 5yys
TitleCryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (FKP)in Bacteroides fragilis
ComponentsL-fucokinase, L-fucose-1-P guanylyltransferase
KeywordsTRANSFERASE / bifunctional / kinase / ATP / GTP
Function / homology
Function and homology information


nucleotidyltransferase activity / kinase activity / ATP binding
Similarity search - Function
L-fucokinase / L-fucokinase / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Bifunctional fucokinase/L-fucose-1-P-guanylyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, J. / Hu, H. / Liu, Y. / Zhou, Q. / Wu, P. / Yan, N. / Wang, H.W. / Wu, J.W. / Sun, L.
CitationJournal: Protein Cell / Year: 2019
Title: Cryo-EM structure of L-fucokinase/GDP-fucose pyrophosphorylase (FKP) in Bacteroides fragilis.
Authors: Ying Liu / Huifang Hu / Jia Wang / Qiang Zhou / Peng Wu / Nieng Yan / Hong-Wei Wang / Jia-Wei Wu / Linfeng Sun /
History
DepositionDec 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: L-fucokinase, L-fucose-1-P guanylyltransferase
B: L-fucokinase, L-fucose-1-P guanylyltransferase
C: L-fucokinase, L-fucose-1-P guanylyltransferase
D: L-fucokinase, L-fucose-1-P guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)423,1314
Polymers423,1314
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6440 Å2
ΔGint-20 kcal/mol
Surface area149300 Å2

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Components

#1: Protein
L-fucokinase, L-fucose-1-P guanylyltransferase


Mass: 105782.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacteroides fragilis (bacteria) / References: UniProt: Q58T34

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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: FKP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacteroides fragilis (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96749 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01624592
ELECTRON MICROSCOPYf_angle_d2.24733488
ELECTRON MICROSCOPYf_dihedral_angle_d12.20214724
ELECTRON MICROSCOPYf_chiral_restr0.13832
ELECTRON MICROSCOPYf_plane_restr0.0144340

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