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- PDB-9j4b: Crystal structure of thio-glucose complexed GH1 beta-glucosidase ... -

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Basic information

Entry
Database: PDB / ID: 9j4b
TitleCrystal structure of thio-glucose complexed GH1 beta-glucosidase (UnBGl1)
ComponentsBeta-glucosidase
KeywordsHYDROLASE / inhibitor / thio-glucose / GH1 / beta-glucosidase
Function / homology1-thio-beta-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 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)53,4859
Polymers52,8401
Non-polymers6458
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.150, 65.710, 137.660
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-GS1 / 1-thio-beta-D-glucopyranose / 1-thio-beta-D-glucose / 1-thio-D-glucose / 1-thio-glucose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
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 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→40 Å / Num. obs: 49212 / % possible obs: 99.4 % / Redundancy: 3.49 % / CC1/2: 0.999 / Net I/σ(I): 26.38
Reflection shellResolution: 1.73→1.83 Å / Mean I/σ(I) obs: 7.32 / Num. unique obs: 14085 / CC1/2: 0.968 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→38.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.559 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18065 2461 5 %RANDOM
Rwork0.14693 ---
obs0.14862 46751 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.542 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.73→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 35 524 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123740
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163349
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.8185126
X-RAY DIFFRACTIONr_angle_other_deg0.6941.7647693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5455472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.55539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18310534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02910
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_it1.5071.551843
X-RAY DIFFRACTIONr_mcbond_other1.5071.5481842
X-RAY DIFFRACTIONr_mcangle_it2.0322.7832306
X-RAY DIFFRACTIONr_mcangle_other2.0342.7852307
X-RAY DIFFRACTIONr_scbond_it2.7731.8121897
X-RAY DIFFRACTIONr_scbond_other2.7191.7891882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other43.1582789
X-RAY DIFFRACTIONr_long_range_B_refined4.88319.984420
X-RAY DIFFRACTIONr_long_range_B_other4.75317.054276
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
Rfree0.19 176 -
Rwork0.161 3343 -
obs--98.49 %

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