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- PDB-33fe: Crystal Structure of the beta-Glucosidase BglA9 in Complex with t... -

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Basic information

Entry
Database: PDB / ID: 33fe
TitleCrystal Structure of the beta-Glucosidase BglA9 in Complex with the Inhibitor Conduritol B Epoxide
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-Glucosidase BglA9 / Complex / Inhibitor / Conduritol B Epoxide
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / 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
(1R,2R,3S,4S,5S,6S)-CYCLOHEXANE-1,2,3,4,5,6-HEXOL / Beta-glucosidase
Similarity search - Component
Biological speciesAnoxybacillus ayderensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRahman, U.U. / Sagmeister, T. / Grininger, C. / Gruber, K. / Khan, S.
Funding support Austria, Pakistan, 3items
OrganizationGrant numberCountry
Other governmentMPC-2025-01016 Austria
Other government Austria
Other governmentPSF-TUBITAK/Med/C-QAU (15) Pakistan
CitationJournal: To Be Published
Title: Crystal Structure of the beta-Glucosidase BglA9 in Complex with the Inhibitor Conduritol B Epoxide
Authors: Rahman, U.U. / Sagmeister, T. / Grininger, C. / Gruber, K. / Khan, S.
History
DepositionAug 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2663
Polymers54,0621
Non-polymers2042
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.441, 99.441, 67.394
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Beta-glucosidase


Mass: 54061.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus ayderensis (bacteria) / Gene: JV16_01116 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D0G9C2, beta-glucosidase
#2: Chemical ChemComp-CBU / (1R,2R,3S,4S,5S,6S)-CYCLOHEXANE-1,2,3,4,5,6-HEXOL


Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Drop setup: 200 nl Protein + 200 nl Condition + 50 nl Seeding stock Protein: 7 mg/ml in 50 mM Tris-HCl, 300 mM NaCl, pH 7.5, premixed with 5x molar excess of Conduritol beta-epoxide (CBE) ...Details: Drop setup: 200 nl Protein + 200 nl Condition + 50 nl Seeding stock Protein: 7 mg/ml in 50 mM Tris-HCl, 300 mM NaCl, pH 7.5, premixed with 5x molar excess of Conduritol beta-epoxide (CBE) Condition: 0.2 M NaCl, 0.1 M MES, 45 % v/v Pentaerythritol propoxylate (5/4 PO/OH), pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 1, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.74→53.13 Å / Num. obs: 70789 / % possible obs: 92 % / Redundancy: 2.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.068 / Net I/σ(I): 4.1
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4135 / CC1/2: 0.649

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (REFMACAT 0.4.126)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→53.13 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 3500 -RANDOM
Rwork0.1535 ---
obs-70785 91.99 %-
Displacement parametersBiso mean: 17.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.74→53.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 12 288 4005
LS refinement shellResolution: 1.74→1.802 Å
RfactorNum. reflection% reflection
Rfree0.3072 369 -
Rwork0.2963 7487 -
obs--98.34 %
Refinement TLS params.Origin x: 25.587 Å / Origin y: -41.958 Å / Origin z: -7.304 Å
111213212223313233
T0.0051 Å2-0.0013 Å20.0109 Å2-0.0026 Å2-0.0196 Å2--0.3456 Å2
L1.6935 °20.7863 °2-0.0939 °2-1.4362 °2-0.1366 °2--0.603 °2
S-0.0017 Å °-0.0673 Å °-0.0096 Å °-0.0673 Å °-0.0172 Å °0.0104 Å °-0.0096 Å °0.0104 Å °0.0189 Å °

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