+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36944 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | the alpha-galactosidase 5 with inhibitor ABP2 | |||||||||
Map data | this is the map of alpha-galactosidases 5 with ABP2. | |||||||||
Sample |
| |||||||||
Keywords | alpha-galactosidase / HYDROLASE / inhibitor ABP2 | |||||||||
Function / homology | Function and homology information alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process Similarity search - Function | |||||||||
Biological species | Blautia pseudococcoides (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Li YW / Ru YX | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Activity-Based Meta proteomics Drives Discovery and Enzymological Characterization of Novel alpha-galactosidases in the Gut Microbiome Authors: Li YW / Ru YX | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_36944.map.gz | 28.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-36944-v30.xml emd-36944.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36944_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_36944.png | 131.8 KB | ||
Filedesc metadata | emd-36944.cif.gz | 5.6 KB | ||
Others | emd_36944_half_map_1.map.gz emd_36944_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36944 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36944 | HTTPS FTP |
-Validation report
Summary document | emd_36944_validation.pdf.gz | 941.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_36944_full_validation.pdf.gz | 940.9 KB | Display | |
Data in XML | emd_36944_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_36944_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36944 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36944 | HTTPS FTP |
-Related structure data
Related structure data | 8k7vMC 8k1aC 8k7uC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_36944.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | this is the map of alpha-galactosidases 5 with ABP2. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: this is half map 1.
File | emd_36944_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | this is half map 1. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: this is half map 2.
File | emd_36944_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | this is half map 2. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Tetramer complex of alpha-galactosidase 5 with ABP2
Entire | Name: Tetramer complex of alpha-galactosidase 5 with ABP2 |
---|---|
Components |
|
-Supramolecule #1: Tetramer complex of alpha-galactosidase 5 with ABP2
Supramolecule | Name: Tetramer complex of alpha-galactosidase 5 with ABP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Blautia pseudococcoides (bacteria) |
-Macromolecule #1: Alpha-galactosidase
Macromolecule | Name: Alpha-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Blautia pseudococcoides (bacteria) |
Molecular weight | Theoretical: 88.017266 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
-Macromolecule #2: 8-azido-1-((1S,2S,3S,4S,5R,6S)-2,3,4-trihydroxy-5-(hydroxymethyl)...
Macromolecule | Name: 8-azido-1-((1S,2S,3S,4S,5R,6S)-2,3,4-trihydroxy-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptan-7-yl)octan-1-one type: ligand / ID: 2 / Number of copies: 4 / Formula: VQX |
---|---|
Molecular weight | Theoretical: 342.391 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |