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- PDB-9j42: Crystal structure of Glucsoe bound glucose tolerant GH1 beta-gluc... -

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Basic information

Entry
Database: PDB / ID: 9j42
TitleCrystal structure of Glucsoe bound glucose tolerant GH1 beta-glucosidase mutant (UnBGl1_C188V)
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / GH1 / Glucose / glucose tolerant
Function / homologybeta-D-glucopyranose / PHOSPHATE ION / :
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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)53,2914
Polymers52,8361
Non-polymers4553
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint0 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 66.980, 138.640
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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
#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.: 572 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
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 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 48288 / % possible obs: 96.9 % / Redundancy: 7.03 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.31
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 6.64 / Num. unique obs: 7023 / CC1/2: 0.953 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→38.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.135 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19115 2415 5 %RANDOM
Rwork0.15377 ---
obs0.15566 45873 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.219 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.75→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 29 574 4169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123750
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163367
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6615139
X-RAY DIFFRACTIONr_angle_other_deg0.5431.5797726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.125540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44310529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02920
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_it1.2271.3211853
X-RAY DIFFRACTIONr_mcbond_other1.2061.3181852
X-RAY DIFFRACTIONr_mcangle_it1.7732.372323
X-RAY DIFFRACTIONr_mcangle_other1.7792.3722324
X-RAY DIFFRACTIONr_scbond_it1.9491.521897
X-RAY DIFFRACTIONr_scbond_other1.9381.5151894
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9732.6812808
X-RAY DIFFRACTIONr_long_range_B_refined4.5617.374559
X-RAY DIFFRACTIONr_long_range_B_other4.2614.214361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 165 -
Rwork0.196 3126 -
obs--90.51 %

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