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Yorodumi- EMDB-42680: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42680 | |||||||||
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Title | Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 | |||||||||
Map data | deepenhancer map | |||||||||
Sample |
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Keywords | 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 Function and homology information | |||||||||
Biological species | Enterobacter hormaechei (CDC Enteric Group 75) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Briganti L / Godoy AS / Capetti CCM / Portugal RV / Polikarpov I | |||||||||
Funding support | Brazil, 1 items
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Citation | Journal: To Be Published 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 | emd_42680.map.gz | 203.4 MB | EMDB map data format | |
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Header (meta data) | emd-42680-v30.xml emd-42680.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42680_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_42680.png | 76.4 KB | ||
Filedesc metadata | emd-42680.cif.gz | 5.4 KB | ||
Others | emd_42680_additional_1.map.gz emd_42680_additional_2.map.gz emd_42680_half_map_1.map.gz emd_42680_half_map_2.map.gz | 121 MB 1.7 MB 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42680 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42680 | HTTPS FTP |
-Related structure data
Related structure data | 8uwsMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42680.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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 |
-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: Enterobacter hormaechei (CDC Enteric Group 75) |
-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: Enterobacter hormaechei (CDC Enteric Group 75) |
Molecular weight | Theoretical: 61.000953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |