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- EMDB-34918: cellodextrin phosphorylase stable variant from Clostridium thermo... -

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Basic information

Entry
Database: EMDB / ID: EMD-34918
Titlecellodextrin phosphorylase stable variant from Clostridium thermocellum
Map data
Sample
  • Complex: cellodextrin phosphorylase dimer
    • Protein or peptide: Cellodextrin phosphorylase
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordscellulose / phosphorolysis / synthesis / CARBOHYDRATE
Function / homology
Function and homology information


glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolase 94 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Cellodextrin phosphorylase
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsKuga T / Sunagawa N / Igarashi K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12566 Japan
CitationJournal: To Be Published
Title: 11 cysteine-to-serine mutations improve the stability of cellodextrin phosphorylase
Authors: Kuga T / Sunagawa N / Igarashi K
History
DepositionDec 8, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34918.png

Downloads & links

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Map

FileDownload / File: emd_34918.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-0.265144 - 0.82752305
Average (Standard dev.)0.00045236034 (±0.014560304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34918_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34918_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cellodextrin phosphorylase dimer

EntireName: cellodextrin phosphorylase dimer
Components
  • Complex: cellodextrin phosphorylase dimer
    • Protein or peptide: Cellodextrin phosphorylase
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: cellodextrin phosphorylase dimer

SupramoleculeName: cellodextrin phosphorylase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Cellodextrin phosphorylase

MacromoleculeName: Cellodextrin phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria) / Strain: YM4
Molecular weightTheoretical: 112.736172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 316 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Particle selectionNumber selected: 9582559
Startup modelType of model: INSILICO MODEL / In silico model: model was generated by using Alphafold2
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.0) / Number images used: 998544
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.0)
FSC plot (resolution estimation)

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