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Yorodumi- EMDB-34504: cryo-EM structure of cellodextrin phosphorylase from Clostridium ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34504 | |||||||||
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Title | cryo-EM structure of cellodextrin phosphorylase from Clostridium thermocellum | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cellulose / cellodextrin / phosphorolysis / synthesis / CARBOHYDRATE | |||||||||
Function / homology | Function and homology information glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Acetivibrio thermocellus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Kuga T / Sunagawa N / Igarashi K | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: To Be Published Title: structure and dynamics of cellodextrin phosphorylase from Clostridium thermocellum determine chain length and crystalline packing of highly ordered cellulose II synthesized in vitro Authors: 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_34504.map.gz | 217.9 MB | EMDB map data format | |
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Header (meta data) | emd-34504-v30.xml emd-34504.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34504_fsc.xml | 21.8 KB | Display | FSC data file |
Images | emd_34504.png | 78.5 KB | ||
Filedesc metadata | emd-34504.cif.gz | 6.2 KB | ||
Others | emd_34504_half_map_1.map.gz emd_34504_half_map_2.map.gz | 391.7 MB 391.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34504 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34504 | HTTPS FTP |
-Validation report
Summary document | emd_34504_validation.pdf.gz | 800.4 KB | Display | EMDB validaton report |
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Full document | emd_34504_full_validation.pdf.gz | 800 KB | Display | |
Data in XML | emd_34504_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | emd_34504_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34504 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34504 | HTTPS FTP |
-Related structure data
Related structure data | 8h6hMC 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_34504.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Half map: #2
File | emd_34504_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34504_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimeric structure of cellodextrin phosphorylase from Clostrid...
Entire | Name: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP) |
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Components |
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-Supramolecule #1: Homodimeric structure of cellodextrin phosphorylase from Clostrid...
Supramolecule | Name: Homodimeric structure of cellodextrin phosphorylase from Clostridium thermocellum (CtCDP) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4 |
Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: Cellodextrin phosphorylase
Macromolecule | Name: Cellodextrin phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acetivibrio thermocellus (bacteria) |
Molecular weight | Theoretical: 112.599523 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVTKVTARNN KITPVELLNQ KFGNKINLGN FADAVFTDAA FKNVAGIANL PMKAPVMQVL MENCIVSKYL KQFVPDRSVC FVEEGQKFY IVLEDGQKIE VPEDVNKALK ATVSDVKHWA GYLTEDGEHV IDLLKPAPGP HFYVNLLIGN RLGFKRTLQT T PKSVVDRF ...String: MVTKVTARNN KITPVELLNQ KFGNKINLGN FADAVFTDAA FKNVAGIANL PMKAPVMQVL MENCIVSKYL KQFVPDRSVC FVEEGQKFY IVLEDGQKIE VPEDVNKALK ATVSDVKHWA GYLTEDGEHV IDLLKPAPGP HFYVNLLIGN RLGFKRTLQT T PKSVVDRF GRGSFRSHAA TQVLATRFDM RQEENGFPAN RQFYLYEDGK QIFYSALIDD NIVEATCKHS CNRTVIKYKT AC NLEITRT IFLVPHKKGF PLATELQRIE IKNASDKARN LSITYTGMFG TGAVHAIFED VTYTNVIMQS AALYNDKGEF IGI TPDYYP EEFKQDTRFV TMIVRNGDEK SFPQSFCTDY NDFVGTGTLE HPAGGCNLNN KLNRKGPGFF ALGAPFTVEP GKTV IIDTF TGLSSSKDNE NYSDAVMLRE LDNLLRYFEK SESVEETLNE IINFHENYGK YFQFNTGNKL FDSGFNRNLA FQVLY QTFM SRSFGQTQKG YREIGFREIQ DLFASMYYFI NIGYQDFVKE LLFEWTANVY KMGYANHNFY WVGKQPGLYS DDSLWL LQA YYRYIIYTKD TSVLNEEVPV ADGNNEKRAV RETLKAIIQY SACISVGDHG LPLLDLADWN DCLKIDSNSI DGATKEK LY YEQLKKTNGK YGDRFMSDYS ESVMNAFLLK LAIDHLAEIA TLDNDTQLAQ QMSELSKEVT DRIQKHAWKE NFFARVLI N RYKDGSYTYL GAKGDKLSAD PNIDGVYFLN SFAWSVLSDV ATDEQIAIMV DVIKKHLLTP YGLRLVTPAD LNKIANDTA TGHYFFGDRE NGAVFKHASM MAVAALIKAA KKVKDNELAK EMARIAYFMI DLVLPYKNLE NPFQVAGNPR ICTQYINTDT GENIGPLLS GTATWLNLNL ISLAGIEYTR DGISFNPILR EEETQLNFTL KAPKCSYKFS ITKPVGFARM ESSEYELFVD G QKIDNTVI PMYTDEKEHI VTLKFKHHHH HH UniProtKB: Cellodextrin phosphorylase |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.0 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM Tris-HCl, 120 mM NaCl, 0.1 mM DTT | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |