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- PDB-8z2y: High-resolution crystal structure of exo-beta-(1,3)-glucanase fro... -

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Basic information

Entry
Database: PDB / ID: 8z2y
TitleHigh-resolution crystal structure of exo-beta-(1,3)-glucanase from Aspergillus oryzae (AoBgl) as a complex with glucose
ComponentsGlucan 1,3-beta-glucosidase A
KeywordsHYDROLASE / cellobiose / glucose / exoglucanase / Aspergillus oryzae / GH5 / laminarin / laminaritriose
Function / homology
Function and homology information


glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / cell wall organization / cell surface / extracellular region / metal ion binding
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / Glucan 1,3-beta-glucosidase A
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBanerjee, B. / Kamale, C.K. / Suryawanshi, A.B. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR41982/PBD/26/822/2021 India
CitationJournal: Febs Lett. / Year: 2025
Title: Crystal structures of Aspergillus oryzae exo-beta-(1,3)-glucanase reveal insights into oligosaccharide binding, recognition, and hydrolysis.
Authors: Banerjee, B. / Kamale, C.K. / Suryawanshi, A.B. / Dasgupta, S. / Noronha, S. / Bhaumik, P.
History
DepositionApr 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucan 1,3-beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9078
Polymers45,2421
Non-polymers6657
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.290, 81.290, 114.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Glucan 1,3-beta-glucosidase A / Exo-1 / 3-beta-glucanase 1 / 3-beta-glucanase A


Mass: 45242.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: exgA, exg1, AO090003000990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7Z9L3, glucan 1,3-beta-glucosidase
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 520 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 134619 / % possible obs: 98.3 % / Redundancy: 10.17 % / CC1/2: 0.999 / Net I/σ(I): 13.72
Reflection shellResolution: 1.2→1.4 Å / Num. unique obs: 48574 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→19.53 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.479 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18505 6709 5 %RANDOM
Rwork0.16101 ---
obs0.1622 127482 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å2-0 Å2
3---2 Å2
Refinement stepCycle: 1 / Resolution: 1.2→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 42 515 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162760
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.6354206
X-RAY DIFFRACTIONr_angle_other_deg0.6361.5756372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.135512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0810464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
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_it0.7160.8711536
X-RAY DIFFRACTIONr_mcbond_other0.7120.8711536
X-RAY DIFFRACTIONr_mcangle_it0.9691.5691921
X-RAY DIFFRACTIONr_mcangle_other0.9681.5711922
X-RAY DIFFRACTIONr_scbond_it1.1031.0431558
X-RAY DIFFRACTIONr_scbond_other1.1021.0431559
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4911.8262284
X-RAY DIFFRACTIONr_long_range_B_refined3.93515.873984
X-RAY DIFFRACTIONr_long_range_B_other2.57811.313785
X-RAY DIFFRACTIONr_rigid_bond_restr4.52735854
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 446 -
Rwork0.378 8481 -
obs--89.37 %

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