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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | the wild-typed alpha-galactosidase 5 | |||||||||
![]() | This map is the wild type of AGAL5 | |||||||||
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![]() | alpha-Galactosidase / HYDROLASE | |||||||||
Function / homology | ![]() alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
![]() | Li YW / Ru YX | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Activity-Based Meta proteomics Drives Discovery and Enzymological Characterization of Novel alpha-galactosidases in the Gut Microbiome Authors: Li YW / Ru YX | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 94.3 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 23.2 MB 23.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k1aMC 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 | This map is the wild type of AGAL5 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: This is the half map 2
File | emd_36790_half_map_1.map | ||||||||||||
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Annotation | This is the half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: This is the half map 1
File | emd_36790_half_map_2.map | ||||||||||||
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Annotation | This is the half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Tetramer complex of alpha-galactosidase 5
Entire | Name: Tetramer complex of alpha-galactosidase 5 |
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Components |
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-Supramolecule #1: Tetramer complex of alpha-galactosidase 5
Supramolecule | Name: Tetramer complex of alpha-galactosidase 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Alpha-galactosidase
Macromolecule | Name: Alpha-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 88.017266 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAVIFHEKTK EFHIFNREVS YLMRIMENGQ LENLYYGKVI RDKEDFGYLH EEAMRSQMSV CIPEPGILSM QYTRQEYPVY GTGDYRSPA LTVLQENGSR LVDFSYVSHE IYKGKKGIPP LPSTYAESED EAETLEVTLH DQVTDTDLVL TYTIYEDYPV I TRNARFEQ ...String: MAVIFHEKTK EFHIFNREVS YLMRIMENGQ LENLYYGKVI RDKEDFGYLH EEAMRSQMSV CIPEPGILSM QYTRQEYPVY GTGDYRSPA LTVLQENGSR LVDFSYVSHE IYKGKKGIPP LPSTYAESED EAETLEVTLH DQVTDTDLVL TYTIYEDYPV I TRNARFEQ KGEQKIVLER AMSASVEFLD MDYELVQLSG AWSRERYVKN RKLEMGIQSV HSLNGTCGGA EHNPFIALKR PQ TTENQGE VYGFSLVYSG NFLAQAEVST FDMTRVMLGI NPEDFSWELN QGESFQTPEV VMVYSDRGLN KMSQAYHRLY RTR LMRVTW RDKARPILLN NWEATYFDFN EEKILKIAEK AKEAGVELFV LDDGWFGARN DDYRGLGDWY VNLEKLPDGI AGLS RKVEA LGLKFGLWVE LEMVNKDSDL YRAHPDWLIG APDRFESHAR HQHVLDFSRK EVVDYIYKMI AKVLRESSIS YIKWD MNRY MTEPYSRGAD ASQQGKVMHK YILGVYDLYT RLTTEFPEIL FESCASGGAR FDPAMLYFAP QTWTSDDTDA SERTKI QYG TSYVYPVVSM GSHVSAVPNH QMHRMTPIET RANVAYFGTF GYELDLNLLS EAELESVKKQ IAFMKEYREL IQVDGDF YR LLSPFEGNET AWMVVAQDKS RAVAAFYQRM NKVNASWIRF KLQGLDAGTL YEVSCDMAPS ASYDESLAKI YGIQTEEN M VKTYRAYGDE LMQVGIPIDR EDLNKKGGDF ASLLYTLKKV TD UniProtKB: Alpha-galactosidase |
-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: GATAN K3 (6k 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |