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- PDB-8znw: Crystal structure of beta-glucosidase Cba3 from Cellulomonas biaz... -

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Basic information

Entry
Database: PDB / ID: 8znw
TitleCrystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea in complex with glucose
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glucosidase / Cellulomonas biazotea / glucose
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / 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
beta-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesCellulomonas biazotea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, D. / Kim, I.J. / Nam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1I1A1A01072158 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Glucose binding to the gatekeeper region induces the glucose stimulation of beta-glucosidase Cba3 from Cellulomonas biazotea.
Authors: Kim, D. / Nam, K.H. / Kim, I.J.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name

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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)48,3643
Polymers48,0031
Non-polymers3602
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint3 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.080, 72.354, 78.381
Angle α, β, γ (deg.)90.00, 108.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-972-

HOH

31A-985-

HOH

41A-1050-

HOH

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Components

#1: Protein Beta-glucosidase


Mass: 48003.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas biazotea (bacteria) / Gene: cba3, bglB, CBZ_21620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1C1T5, beta-glucosidase
#2: 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 natural 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Na-cacodylate, PEG 8000, calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35911 / % possible obs: 98.6 % / Redundancy: 5.5 % / CC1/2: 0.964 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1755 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.264 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18783 1838 5.1 %RANDOM
Rwork0.1544 ---
obs0.15614 34073 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0.93 Å2
2---0.64 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 24 467 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163050
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6594651
X-RAY DIFFRACTIONr_angle_other_deg0.5521.5787009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.516525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74610448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2490.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
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_it1.5861.6281710
X-RAY DIFFRACTIONr_mcbond_other1.5841.6281710
X-RAY DIFFRACTIONr_mcangle_it2.4842.9192134
X-RAY DIFFRACTIONr_mcangle_other2.4862.922135
X-RAY DIFFRACTIONr_scbond_it2.2651.7831683
X-RAY DIFFRACTIONr_scbond_other2.2641.7841684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6183.1852518
X-RAY DIFFRACTIONr_long_range_B_refined6.26417.844116
X-RAY DIFFRACTIONr_long_range_B_other5.84216.513921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 126 -
Rwork0.23 2459 -
obs--95.6 %

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