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- PDB-9j41: Crystal Structure of glucose tolerant beta-glucosidase UnBGl1 mut... -

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Basic information

Entry
Database: PDB / ID: 9j41
TitleCrystal Structure of glucose tolerant beta-glucosidase UnBGl1 mutant (C188V)
ComponentsBeta-glucosidase
KeywordsHYDROLASE / GH1 / beta-glucosidase / Glucose tolerant
Function / homologyPHOSPHATE ION / :
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSuryawanshi, A.B. / Bedi, R.K. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR41982/PBD/26/822/2021 India
CitationJournal: Biorxiv / Year: 2025
Title: Rewiring Catalytic Craters: A Path for Engineering beta-Glucosidases to Improve Glucose Tolerance
Authors: Suryawanshi, A.B. / Bedi, R.K. / Pawar, M. / Noronha, S. / Bhaumik, P.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 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)52,9663
Polymers52,8361
Non-polymers1302
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-14 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.880, 66.270, 138.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-glucosidase


Mass: 52835.652 Da / Num. of mol.: 1 / Mutation: C188V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) soil metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4I4U1, beta-glucosidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2

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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: 0.97949 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 116123 / % possible obs: 93.6 % / Redundancy: 2.54 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.69
Reflection shellResolution: 1.3→1.4 Å / Rmerge(I) obs: 0.398 / Num. unique obs: 43539 / CC1/2: 0.787 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→28.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.084 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18772 5806 5 %RANDOM
Rwork0.16807 ---
obs0.16904 110314 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.616 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å2-0 Å2
2---1.4 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.3→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 6 593 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123785
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163432
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.8255193
X-RAY DIFFRACTIONr_angle_other_deg0.6891.7717882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.924546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25310554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
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_it3.3971.111862
X-RAY DIFFRACTIONr_mcbond_other3.3911.1081861
X-RAY DIFFRACTIONr_mcangle_it4.6082.0032333
X-RAY DIFFRACTIONr_mcangle_other4.6132.0042334
X-RAY DIFFRACTIONr_scbond_it5.0521.2931923
X-RAY DIFFRACTIONr_scbond_other4.9961.2911920
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8922.2832838
X-RAY DIFFRACTIONr_long_range_B_refined14.28615.744541
X-RAY DIFFRACTIONr_long_range_B_other11.54612.684335
X-RAY DIFFRACTIONr_rigid_bond_restr5.00337217
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 424 -
Rwork0.276 8058 -
obs--98.55 %

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