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Yorodumi- EMDB-34918: cellodextrin phosphorylase stable variant from Clostridium thermo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34918 | |||||||||
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Title | cellodextrin phosphorylase stable variant from Clostridium thermocellum | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cellulose / phosphorolysis / synthesis / CARBOHYDRATE | |||||||||
Function / homology | Function and homology information transferase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Acetivibrio thermocellus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.28 Å | |||||||||
Authors | Kuga T / Sunagawa N / Igarashi K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: To Be Published Title: 11 cysteine-to-serine mutations improve the stability of cellodextrin phosphorylase 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_34918.map.gz | 219.8 MB | EMDB map data format | |
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Header (meta data) | emd-34918-v30.xml emd-34918.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34918_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_34918.png | 139.4 KB | ||
Filedesc metadata | emd-34918.cif.gz | 6.1 KB | ||
Others | emd_34918_half_map_1.map.gz emd_34918_half_map_2.map.gz | 391.3 MB 391.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34918 | HTTPS FTP |
-Related structure data
Related structure data | 8hnuMC 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_34918.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_34918_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34918_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : cellodextrin phosphorylase dimer
Entire | Name: cellodextrin phosphorylase dimer |
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Components |
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-Supramolecule #1: cellodextrin phosphorylase dimer
Supramolecule | Name: cellodextrin phosphorylase dimer / 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) / Strain: YM4 |
Molecular weight | Theoretical: 112.736172 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGITKVTARN NKITPVELLN QKFGNKINLG NFADAVFTDA AFKNVAGIAN LPMKAPVMQV LMENSIVSKY LKQFVPDRSV SFVEEGQKF YIVLEDGQKI EVPEDVNKAL KATVSDVKHW AGYLTEDGEH VIDLLKPAPG PHFYVNLLIG NRLGFKRTLQ T TPKSVVDR ...String: MGITKVTARN NKITPVELLN QKFGNKINLG NFADAVFTDA AFKNVAGIAN LPMKAPVMQV LMENSIVSKY LKQFVPDRSV SFVEEGQKF YIVLEDGQKI EVPEDVNKAL KATVSDVKHW AGYLTEDGEH VIDLLKPAPG PHFYVNLLIG NRLGFKRTLQ T TPKSVVDR FGRGSFRSHA ATQVLATRFD MRQEENGFPA NRQFYLYEDG KQIFYSALID DNIVEATSKH SSNRTVIKYK TA SNLEITR TIFLVPHKKG FPLATELQRI EIKNASDKAR NLSITYTGMF GTGAVHAIFE DVTYTNVIMQ SAALYNDKGE FIG ITPDYY PEEFKQDTRF VTMIVRNGDE KSFPQSFSTD YNDFVGTGTL EHPAGGSNLN NKLNRKGPGF FALGAPFTVE PGKT VIIDT FTGLSSSKDN ENYSDAVMLR ELDNLLRYFE KSESVEETLN EIINFHENYG KYFQFNTGNK LFDSGFNRNL AFQVL YQTF MSRSFGQTQK GYREIGFREI QDLFASMYYF INIGYQDFVK ELLFEWTANV YKMGYANHNF YWVGKQPGLY SDDSLW LLQ AYYRYIIYTK DTSVLNEEVP VADGNNEKRA VRETLKAIIQ YSASISVGDH GLPLLDLADW NDSLKIDSNS IDGATKE KL YYEQLKKTNG KYGDRFMSDY SESVMNAFLL KLAIDHLAEI ATLDNDTQLA QQMSELSKEV TDRIQKHAWK ENFFARVL I NRYKDGSYTY LGAKGDKLSA DPNIDGVYFL NSFAWSVLSD VATDEQIAIM VDVIKKHLLT PYGLRLVTPA DLNKIANDT ATGHYFFGDR ENGAVFKHAS MMAVAALIKA AKKVKDNELA KEMARIAYFM IDLVLPYKNL ENPFQVAGNP RISTQYINTD TGENIGPLL SGTATWLNLN LISLAGIEYT RDGISFNPIL REEETQLNFT LKAPKSSYKF SITKPVGFAR MESSEYELFV D GQKIDNTV IPMYTDEKEH IVTLKFKLEH HHHHH 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 |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 316 / 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 | 3.0 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |