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- PDB-8znv: Crystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea -

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Basic information

Entry
Database: PDB / ID: 8znv
TitleCrystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glucosidase / Cellulomonas biazotea
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
Biological speciesCellulomonas biazotea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: To Be Published
Title: Crystal structure of ?-glucosidase Cba3 from Cellulomonas biazotea
Authors: Kim, D. / Kim, I.J. / Nam, K.H.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: 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)48,0952
Polymers48,0031
Non-polymers921
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.391, 72.282, 78.446
Angle α, β, γ (deg.)90.00, 108.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-933-

HOH

21A-1010-

HOH

31A-1085-

HOH

41A-1087-

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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
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: 1.7→50 Å / Num. obs: 50394 / % possible obs: 98.5 % / Redundancy: 5.4 % / CC1/2: 0.994 / Net I/σ(I): 19.94
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2530 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.14 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.93 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17714 2430 4.8 %RANDOM
Rwork0.14625 ---
obs0.14771 47819 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.401 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2-0 Å2-0.81 Å2
2---0.13 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 6 496 3777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123379
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163045
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6574629
X-RAY DIFFRACTIONr_angle_other_deg0.561.5786992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.468525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7510448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
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_it1.8571.6791714
X-RAY DIFFRACTIONr_mcbond_other1.8461.6781714
X-RAY DIFFRACTIONr_mcangle_it2.6553.0122139
X-RAY DIFFRACTIONr_mcangle_other2.6583.0132140
X-RAY DIFFRACTIONr_scbond_it2.4721.8261665
X-RAY DIFFRACTIONr_scbond_other2.4711.8261666
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7493.2592491
X-RAY DIFFRACTIONr_long_range_B_refined5.89718.934060
X-RAY DIFFRACTIONr_long_range_B_other5.35517.063854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 176 -
Rwork0.225 3528 -
obs--98.33 %

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