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- EMDB-6859: Cryo-EM structure of L-fucokinase,GDP-fucose pyrophosphorylase (F... -

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Basic information

Entry
Database: EMDB / ID: EMD-6859
TitleCryo-EM structure of L-fucokinase,GDP-fucose pyrophosphorylase (FKP) in Bacteroides fragilis
Map data
Sample
  • Complex: FKP
    • Protein or peptide: L-fucokinase, L-fucose-1-P guanylyltransferase
Keywordsbifunctional / kinase / ATP / GTP / TRANSFERASE
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
L-fucokinase/L-fucose-1-P guanylyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang J / Hu H
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, 2017-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 12, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5yys
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6859.png

Downloads & links

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Map

FileDownload / File: emd_6859.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.02450013 - 0.07406046
Average (Standard dev.)0.00037402968 (±0.0030467487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0250.0740.000

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Supplemental data

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Sample components

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Entire : FKP

EntireName: FKP
Components
  • Complex: FKP
    • Protein or peptide: L-fucokinase, L-fucose-1-P guanylyltransferase

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Supramolecule #1: FKP

SupramoleculeName: FKP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroides fragilis (bacteria)

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

MacromoleculeName: L-fucokinase, L-fucose-1-P guanylyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 105.782789 KDa
SequenceString: MQKLLSLPSN LVQSFHELER VNRTDWFCTS DPVGKKLGSG GGTSWLLEEC YNEYSDGATF GEWLEKEKRI LLHAGGQSRR LPGYAPSGK ILTPVPVFRW ERGQHLGQNL LSLQLPLYEK IMSLAPDKLH TLIASGDVYI RSEKPLQSIP EADVVCYGLW V DPSLATHH ...String:
MQKLLSLPSN LVQSFHELER VNRTDWFCTS DPVGKKLGSG GGTSWLLEEC YNEYSDGATF GEWLEKEKRI LLHAGGQSRR LPGYAPSGK ILTPVPVFRW ERGQHLGQNL LSLQLPLYEK IMSLAPDKLH TLIASGDVYI RSEKPLQSIP EADVVCYGLW V DPSLATHH GVFASDRKHP EQLDFMLQKP SLAELESLSK THLFLMDIGI WLLSDRAVEI LMKRSHKESS EELKYYDLYS DF GLALGTH PRIEDEEVNT LSVAILPLPG GEFYHYGTSK ELISSTLSVQ NKVYDQRRIM HRKVKPNPAM FVQNAVVRIP LCA ENADLW IENSHIGPKW KIASRHIITG VPENDWSLAV PAGVCVDVVP MGDKGFVARP YGLDDVFKGD LRDSKTTLTG IPFG EWMSK RGLSYTDLKG RTDDLQAVSV FPMVNSVEEL GLVLRWMLSE PELEEGKNIW LRSEHFSADE ISAGANLKRL YAQRE EFRK GNWKALAVNH EKSVFYQLDL ADAAEDFVRL GLDMPELLPE DALQMSRIHN RMLRARILKL DGKDYRPEEQ AAFDLL RDG LLDGISNRKS TPKLDVYSDQ IVWGRSPVRI DMAGGWTDTP PYSLYSGGNV VNLAIELNGQ PPLQVYVKPC KDFHIVL RS IDMGAMEIVS TFDELQDYKK IGSPFSIPKA ALSLAGFAPA FSAVSYASLE EQLKDFGAGI EVTLLAAIPA GSGLGTSS I LASTVLGAIN DFCGLAWDKN EICQRTLVLE QLLTTGGGWQ DQYGGVLQGV KLLQTEAGFA QSPLVRWLPD HLFTHPEYK DCHLLYYTGI TRTAKGILAE IVSSMFLNSS LHLNLLSEMK AHALDMNEAI QRGSFVEFGR LVGKTWEQNK ALDSGTNPPA VEAIIDLIK DYTLGYKLPG AGGGGYLYMV AKDPQAAVRI RKILTENAPN PRARFVEMTL SDKGFQVSRS

UniProtKB: L-fucokinase/L-fucose-1-P guanylyltransferase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96749
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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