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- PDB-8z2w: Crystal structure of apo- exo-beta-(1,3)-glucanase from Aspergill... -

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Basic information

Entry
Database: PDB / ID: 8z2w
TitleCrystal structure of apo- exo-beta-(1,3)-glucanase from Aspergillus oryzae (AoBgl)
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
: / Glucan 1,3-beta-glucosidase A
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,4033
Polymers45,2421
Non-polymers1612
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.488, 81.488, 115.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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
#2: Chemical ChemComp-A1L0T / 2-methylpropylphosphonic acid


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→70.57 Å / Num. obs: 45212 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.1
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 2452 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→70.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.733 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17175 2283 5.1 %RANDOM
Rwork0.14391 ---
obs0.14533 42888 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.289 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.75→70.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 9 315 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162760
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6354212
X-RAY DIFFRACTIONr_angle_other_deg0.5741.5766372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.676512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27810470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
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_it1.0670.9971555
X-RAY DIFFRACTIONr_mcbond_other1.0610.9971555
X-RAY DIFFRACTIONr_mcangle_it1.5651.7851944
X-RAY DIFFRACTIONr_mcangle_other1.5661.7871945
X-RAY DIFFRACTIONr_scbond_it2.0351.1771540
X-RAY DIFFRACTIONr_scbond_other2.0311.1761538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2392.0582265
X-RAY DIFFRACTIONr_long_range_B_refined5.12611.173782
X-RAY DIFFRACTIONr_long_range_B_other5.12511.173783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 180 -
Rwork0.191 3071 -
obs--98.81 %

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