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- PDB-9j3w: Crystal structure of glucose bound beta-glucosidase UnBGl1 -

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Basic information

Entry
Database: PDB / ID: 9j3w
TitleCrystal structure of glucose bound beta-glucosidase UnBGl1
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / Glucose / Feedback inhibition / Glucose tolerance / GH1
Function / homologybeta-D-glucopyranose / alpha-D-glucopyranose / PHOSPHATE ION / :
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 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 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 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)53,4755
Polymers52,8401
Non-polymers6354
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-1 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.910, 66.180, 138.170
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: 52839.664 Da / Num. of mol.: 1
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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 50247 / % possible obs: 99.4 % / Redundancy: 6.95 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Net I/σ(I): 56.01
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 5305 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→37.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.386 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15576 2513 5 %RANDOM
Rwork0.12829 ---
obs0.12967 47733 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.73→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 41 558 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123792
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163401
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.825201
X-RAY DIFFRACTIONr_angle_other_deg0.6711.7677816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.517539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87110541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1990.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02918
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_it1.1660.9541861
X-RAY DIFFRACTIONr_mcbond_other1.1640.9551861
X-RAY DIFFRACTIONr_mcangle_it1.6051.7112330
X-RAY DIFFRACTIONr_mcangle_other1.6181.7142331
X-RAY DIFFRACTIONr_scbond_it2.1521.181931
X-RAY DIFFRACTIONr_scbond_other2.1371.1761928
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.272.042855
X-RAY DIFFRACTIONr_long_range_B_refined4.9414.184548
X-RAY DIFFRACTIONr_long_range_B_other4.59611.264345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 168 -
Rwork0.138 3194 -
obs--92.11 %

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