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- PDB-9j49: High resolution crystal strucutre of highly glucose tolerant GH1 ... -

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Basic information

Entry
Database: PDB / ID: 9j49
TitleHigh resolution crystal strucutre of highly glucose tolerant GH1 beta-glucosidase (UnBGl1_C188V_H261W)
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: 1.55 Å
AuthorsSuryawanshi, A.B. / 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)53,71510
Polymers52,8841
Non-polymers8329
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-3 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.750, 66.380, 137.490
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: 52883.719 Da / Num. of mol.: 1 / Mutation: C188V/H261W
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
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: 0.97777 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 69348 / % possible obs: 99.7 % / Redundancy: 743 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.42
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 6.17 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 11661 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.89 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.353 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16302 3468 5 %RANDOM
Rwork0.13881 ---
obs0.14 65880 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2---0.16 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.55→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 53 523 4257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123991
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163597
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6635469
X-RAY DIFFRACTIONr_angle_other_deg0.5941.5858266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.391545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26510570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02992
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_it1.2771.0351927
X-RAY DIFFRACTIONr_mcbond_other1.2461.0341926
X-RAY DIFFRACTIONr_mcangle_it1.8471.8522419
X-RAY DIFFRACTIONr_mcangle_other1.8481.8522420
X-RAY DIFFRACTIONr_scbond_it2.321.3012064
X-RAY DIFFRACTIONr_scbond_other2.321.3022065
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5452.2563034
X-RAY DIFFRACTIONr_long_range_B_refined5.24115.034759
X-RAY DIFFRACTIONr_long_range_B_other4.80811.774574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 251 -
Rwork0.229 4773 -
obs--99.21 %

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