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- PDB-8y0l: beta-glucosidase from Thermoascus aurantiacus -

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Basic information

Entry
Database: PDB / ID: 8y0l
Titlebeta-glucosidase from Thermoascus aurantiacus
Componentsbeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / Glycoside hydrolase family 3 / Thermostable enzyme / Thermoascus aurantiacus
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: 2.15 Å
AuthorsMatsuzaki, C. / Katayama, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of beta-glucosidase from Thermoascus aurantiacus
Authors: Matsuzaki, C. / Hidaka, M. / Nakashima, Y. / Honda, Y. / Koyanagi, T. / Ishikawa, K. / Katoh, T. / Kumagai, H. / Katayama, T.
History
DepositionJan 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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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)375,17720
Polymers374,2334
Non-polymers94416
Water58,2243232
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)138.945, 149.752, 175.529
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: 93558.211 Da / Num. of mol.: 4
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.: 12 / 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 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3232 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH7.0, 0.14 M magnesium chloride, 20% 2-propanol, 0.5 mM 1-deoxynojirimycin

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Data collection

DiffractionMean temperature: 100 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: 2.15→50 Å / Num. obs: 198186 / % possible obs: 99.8 % / Redundancy: 4.17 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 11.6
Reflection shellResolution: 2.151→2.207 Å / Rmerge(I) obs: 0.051 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 13698 / R split: 0.236 / Rrim(I) all: 0.179 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→37.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.539 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 9967 5 %RANDOM
Rwork0.16775 ---
obs0.16943 187801 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.499 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.15→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23908 0 56 3232 27196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01224592
X-RAY DIFFRACTIONr_bond_other_d0.0010.01622340
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.833512
X-RAY DIFFRACTIONr_angle_other_deg0.3581.74251476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52653112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.3735124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.777103668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.23576
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0229692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025740
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_it0.4871.78812484
X-RAY DIFFRACTIONr_mcbond_other0.4861.78812484
X-RAY DIFFRACTIONr_mcangle_it0.8913.21115584
X-RAY DIFFRACTIONr_mcangle_other0.8913.21115585
X-RAY DIFFRACTIONr_scbond_it0.4641.84412108
X-RAY DIFFRACTIONr_scbond_other0.4641.84412109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8433.38217929
X-RAY DIFFRACTIONr_long_range_B_refined2.89218.2928784
X-RAY DIFFRACTIONr_long_range_B_other2.89218.2928785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 694 -
Rwork0.208 13698 -
obs--99.12 %

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