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Yorodumi- EMDB-34921: The cryo-EM structure of cellobiose phosphorylase from Clostridiu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34921 | |||||||||
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Title | The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cellobiose phosphorylase / TRANSFERASE | |||||||||
Function / homology | Function and homology information cellobiose phosphorylase / cellobiose phosphorylase activity / cellulose catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Acetivibrio thermocellus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||
Authors | Iriya S / Kuga T / Sunagawa N / Igarashi K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: To Be Published Title: The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum Authors: Iriya S / Kuga T / Sunagawa N / Igarashi K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34921.map.gz | 225.5 MB | EMDB map data format | |
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Header (meta data) | emd-34921-v30.xml emd-34921.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34921_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_34921.png | 89.2 KB | ||
Masks | emd_34921_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-34921.cif.gz | 6 KB | ||
Others | emd_34921_half_map_1.map.gz emd_34921_half_map_2.map.gz | 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34921 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34921 | HTTPS FTP |
-Validation report
Summary document | emd_34921_validation.pdf.gz | 836.7 KB | Display | EMDB validaton report |
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Full document | emd_34921_full_validation.pdf.gz | 836.3 KB | Display | |
Data in XML | emd_34921_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_34921_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34921 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34921 | HTTPS FTP |
-Related structure data
Related structure data | 8ho7MC 8ho9C 8hobC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34921.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34921_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34921_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34921_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cellobiose phosphorylase
Entire | Name: Cellobiose phosphorylase |
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Components |
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-Supramolecule #1: Cellobiose phosphorylase
Supramolecule | Name: Cellobiose phosphorylase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4 |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: Cellobiose phosphorylase
Macromolecule | Name: Cellobiose phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cellobiose phosphorylase |
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Source (natural) | Organism: Acetivibrio thermocellus (bacteria) |
Molecular weight | Theoretical: 93.872453 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MEFGFFDDAN KEYVITVPRT PYPWINYLGT ENFFSLISNT AGGYCFYRDA RLRRITRYRY NNVPIDMGGR YFYIYDNGDF WSPGWSPVK RELESYECRH GLGYTKIAGK RNGIKAEVTF FVPLNYNGEV QKLILKNEGQ DKKKITLFSF IEFCLWNAYD D MTNFQRNF ...String: MEFGFFDDAN KEYVITVPRT PYPWINYLGT ENFFSLISNT AGGYCFYRDA RLRRITRYRY NNVPIDMGGR YFYIYDNGDF WSPGWSPVK RELESYECRH GLGYTKIAGK RNGIKAEVTF FVPLNYNGEV QKLILKNEGQ DKKKITLFSF IEFCLWNAYD D MTNFQRNF STGEVEIEGS VIYHKTEYRE RRNHYAFYSV NAKISGFDSD RDSFIGLYNG FDAPQAVVNG KSNNSVADGW AP IASHSIE IELNPGEQKE YVFIIGYVEN KDEEKWESKG VINKKKAYEM IEQFNTVEKV DKAFEELKSY WNALLSKYFL ESH DEKLNR MVNIWNQYQC MVTFNMSRSA SYFESGIGRG MGFRDSNQDL LGFVHQIPER ARERLLDLAA TQLEDGSAYH QYQP LTKKG NNEIGSNFND DPLWLILATA AYIKETGDYS ILKEQVPFNN DPSKADTMFE HLTRSFYHVV NNLGPHGLPL IGRAD WNDC LNLNCFSTVP DESFQTTTSK DGKVAESVMI AGMFVFIGKD YVKLCEYMGL EEEARKAQQH IDAMKEAILK YGYDGE WFL RAYDDFGRKV GSKENEEGKI FIESQGFCVM AEIGLEDGKA LKALDSVKKY LDTPYGLVLQ NPAFTRYYIE YGEISTY PP GYKENAGIFC HNNAWIICAE TVVGRGDMAF DYYRKIAPAY IEDVSDIHKL EPYVYAQMVA GKDAKRHGEA KNSWLTGT A AWNFVAISQW ILGVKPDYDG LKIDPCIPKA WDGYKVTRYF RGSTYEITVK NPNHVSKGVA KITVDGNEIS GNILPVFND GKTHKVEVIL EHHHHHH UniProtKB: Cellobiose phosphorylase |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 112 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||
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Buffer | pH: 6.5 Component:
Details: 20 mM MES, 70 mM NaCl | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV Details: Vitrification carried out in nitrogen atmosphere.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 2907 / Average exposure time: 5.121 sec. / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |