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- EMDB-42680: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 | |||||||||
![]() | deepenhancer map | |||||||||
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![]() | GH43 / Enterobacter / Beta-Xylosidase / EcXyl43 / HYDROLASE | |||||||||
Function / homology | Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Beta-xylosidase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
![]() | Briganti L / Godoy AS / Capetti CCM / Portugal RV / Polikarpov I | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 Authors: Briganti L / Godoy AS / Polikarpov I | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 203.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 76.4 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() ![]() ![]() | 121 MB 1.7 MB 226.6 MB 226.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 857.5 KB | Display | ![]() |
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Full document | ![]() | 857.1 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uwsMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | deepenhancer map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: cryosparc refinement map
File | emd_42680_additional_1.map | ||||||||||||
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Annotation | cryosparc refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: mask
File | emd_42680_additional_2.map | ||||||||||||
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Annotation | mask | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half B
File | emd_42680_half_map_1.map | ||||||||||||
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Annotation | half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half A
File | emd_42680_half_map_2.map | ||||||||||||
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Annotation | half A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Tetrameric GH43 structure
Entire | Name: Tetrameric GH43 structure |
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Components |
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-Supramolecule #1: Tetrameric GH43 structure
Supramolecule | Name: Tetrameric GH43 structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Beta-xylosidase
Macromolecule | Name: Beta-xylosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 61.000953 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEITNPILTG FNPDPSLCRQ GEDYYIATST FEWFPGVRIY HSRDLKNWTL VSTPLDRVSM LDMKGNPDSG GIWAPCLSYA DGKFWLLYT DVKIVDSPWK NGRNFLVTAP SIEGPWSEPI PMGNGGFDPS LFHDDDGRKY YLYRPWGPRH HSNPHNTIVM Q EFDPQTGT ...String: MEITNPILTG FNPDPSLCRQ GEDYYIATST FEWFPGVRIY HSRDLKNWTL VSTPLDRVSM LDMKGNPDSG GIWAPCLSYA DGKFWLLYT DVKIVDSPWK NGRNFLVTAP SIEGPWSEPI PMGNGGFDPS LFHDDDGRKY YLYRPWGPRH HSNPHNTIVM Q EFDPQTGT LSPERKTLFT GTPLCYTEGA HLYRHAGWYY LMVAEGGTSY EHAVVVLRAK TIDGPYELHP DVTMMTSWHL PE NPLQKSG HGSLLQTHTG EWYMAYLTSR PLRLPGVPLL ASGGRGYCPL GRETGIARIE WRDGWPYVEG GKHAQLTVKG PQV AEQPAA VQGSWRDDFD GSTLDPELQT LRIPFDDTLG SLTARPGYLR LYGNDSLNST FTQSTVARRW QHFIFRAETR MQFS PVHFQ QSAGLTCYYN SKNWSYCFVD YEEGQGRTIK VIQLDHNVPS WPLHEQPIPV PEQAESVWLR VDVDRLVYRY SYSFD GETW HAVPVTYEAW KLSDDYIGGR GFFTGAFVGL HCEDISGDGC HADFDYFTYE PA UniProtKB: Beta-xylosidase |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |