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- PDB-8y0m: beta-glucosidase mutant M279V_T308S_K361R_D433N_N514C -

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Open data


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Basic information

Entry
Database: PDB / ID: 8y0m
Titlebeta-glucosidase mutant M279V_T308S_K361R_D433N_N514C
Componentsbeta-glucosidase
KeywordsHYDROLASE / Thermoascus aurantiacus / beta-glucosidase / Thermostable enzyme / mutant
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
: / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal ...: / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
1-DEOXYNOJIRIMYCIN / beta-glucosidase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsuzaki, C. / Katayama, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Jpn Acad Ser B Phys Biol Sci / Year: 2025
Title: A thermostable and highly active fungal GH3 beta-glucosidase generated by random and saturation mutagenesis.
Authors: Matsuzaki, C. / Hidaka, M. / Nakashima, Y. / Honda, Y. / Koyanagi, T. / Ishikawa, K. / Katoh, T. / Katayama, T. / Kumagai, H.
History
DepositionJan 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-glucosidase
B: beta-glucosidase
C: beta-glucosidase
D: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,00918
Polymers374,1134
Non-polymers89614
Water54,0813002
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.195, 150.165, 174.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
beta-glucosidase


Mass: 93528.195 Da / Num. of mol.: 4 / Mutation: M279V,T308S,K361R,D433N,N514C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Strain: IFO9748 / Gene: bgl1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) / References: UniProt: Q0ZUL0, beta-glucosidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Type: D-saccharide / Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3002 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH7.0, 0.16 M magnesium chloride, 25% 2-propanol, 0.5 mM 1-deoxynojirimycin

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40.2 Å / Num. obs: 160623 / % possible obs: 99.87 % / Redundancy: 4.17 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.359 Å / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 11127 / % possible all: 99.38

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.847 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18024 8008 5 %RANDOM
Rwork0.16186 ---
obs0.16277 153281 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23904 0 54 3002 26960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01224588
X-RAY DIFFRACTIONr_bond_other_d0.0010.01622340
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.833512
X-RAY DIFFRACTIONr_angle_other_deg0.3971.74151460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60853112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.2615128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.581103656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.23580
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0229720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025760
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6172.19212484
X-RAY DIFFRACTIONr_mcbond_other0.6172.19212484
X-RAY DIFFRACTIONr_mcangle_it1.123.93515584
X-RAY DIFFRACTIONr_mcangle_other1.123.93515585
X-RAY DIFFRACTIONr_scbond_it0.5782.26112104
X-RAY DIFFRACTIONr_scbond_other0.5782.26112105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0514.14117929
X-RAY DIFFRACTIONr_long_range_B_refined2.98422.2128679
X-RAY DIFFRACTIONr_long_range_B_other2.98422.2128680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 531 -
Rwork0.2 11174 -
obs--99.38 %

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