[English] 日本語
![](img/lk-miru.gif)
- EMDB-6859: Cryo-EM structure of L-fucokinase,GDP-fucose pyrophosphorylase (F... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-6859 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of L-fucokinase,GDP-fucose pyrophosphorylase (FKP) in Bacteroides fragilis | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | bifunctional / kinase / ATP / GTP / TRANSFERASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Wang J / Hu H | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 9.7 KB 9.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 88.6 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 393.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 392.6 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yysMC ![]() 6860C ![]() 6861C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : FKP
Entire | Name: FKP |
---|---|
Components |
|
-Supramolecule #1: FKP
Supramolecule | Name: FKP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: L-fucokinase, L-fucose-1-P guanylyltransferase
Macromolecule | Name: L-fucokinase, L-fucose-1-P guanylyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 105.782789 KDa |
Sequence | String: 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: Bifunctional fucokinase/L-fucose-1-P-guanylyltransferase |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |