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- PDB-8ztw: CryoEM structure of a GH1 family beta-glucosidase -

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Basic information

Entry
Database: PDB / ID: 8ztw
TitleCryoEM structure of a GH1 family beta-glucosidase
ComponentsMultifunctional glycoside hydrolase
KeywordsHYDROLASE / beta-glucosidase
Function / homology
Function and homology information


glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / lactose catabolic process / glucan catabolic process / beta-galactosidase / beta-glucosidase ...glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / lactose catabolic process / glucan catabolic process / beta-galactosidase / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / protein homotrimerization / xylan catabolic process / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Multifunctional glycoside hydrolase
Similarity search - Component
Biological speciesCaldicellulosiruptor owensensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Ma, L.X. / Cao, Z. / Xing, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
National Science Foundation (NSF, China)32371277 China
CitationJournal: To Be Published
Title: CryoEM structure of a GH1 family beta-glucosidase
Authors: Jiang, W.X. / Cheng, X.Q. / Ma, L.X. / Cao, Z. / Xing, Q.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multifunctional glycoside hydrolase
B: Multifunctional glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)107,0032
Polymers107,0032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Multifunctional glycoside hydrolase / Multifunctional GH / CoGH1A


Mass: 53501.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor owensensis (strain ATCC 700167 / DSM 13100 / OL) (bacteria)
Gene: Calow_0296 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E4Q361, beta-glucosidase, beta-galactosidase, xylan 1,4-beta-xylosidase, glucan 1,4-beta-glucosidase, cellulose 1,4-beta-cellobiosidase (non-reducing end)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: dimer of GH1 family beta-glucosidase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Caldicellulosiruptor owensensis (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148229 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00347804
ELECTRON MICROSCOPYf_angle_d0.568510574
ELECTRON MICROSCOPYf_chiral_restr0.04411072
ELECTRON MICROSCOPYf_plane_restr0.00471358
ELECTRON MICROSCOPYf_dihedral_angle_d4.8911000

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