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- PDB-9jtt: Crystal Structure of Beta-glucosidase from the Indigo-producing P... -

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Basic information

Entry
Database: PDB / ID: 9jtt
TitleCrystal Structure of Beta-glucosidase from the Indigo-producing Plant Polygonum tinctorium
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Beta-glucosidase / Indigo-producing / Polygonum tinctorium / Indigo Dyeing
Function / homologyGlycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / beta-glucosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Chem-1PG / Beta-glucosidase
Function and homology information
Biological speciesPersicaria tinctoria (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYoneda, K. / Himeno, M. / Sakuraba, H. / Ohshima, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Beta-glucosidase from the Indigo-producing Plant Polygonum tinctorium
Authors: Yoneda, K. / Himeno, M. / Sakuraba, H. / Ohshima, T.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9066
Polymers109,3472
Non-polymers5594
Water11,836657
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7962
Polymers54,6731
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1104
Polymers54,6731
Non-polymers4373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.435, 104.059, 99.474
Angle α, β, γ (deg.)90.00, 103.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-glucosidase


Mass: 54673.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persicaria tinctoria (plant) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q9XJ67, beta-glucosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG MME 2000 0.1 M Tris pH8.5 0.2 M Trimethylamine N-Oxide Dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.018 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 1.92→48.56 Å / Num. obs: 75966 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.947 / Rpim(I) all: 0.151 / Rrim(I) all: 0.289 / Χ2: 1.49 / Net I/σ(I): 7.3
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4509 / CC1/2: 0.515 / Rpim(I) all: 0.411 / Rrim(I) all: 0.799 / Χ2: 1.09 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.92→48.4 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / SU B: 5.302 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25157 3729 4.9 %RANDOM
Rwork0.21306 ---
obs0.21498 72248 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.02 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.92→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7532 0 37 657 8226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137773
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177125
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.64110518
X-RAY DIFFRACTIONr_angle_other_deg1.3111.58216411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48822.671423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.277151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1981538
X-RAY DIFFRACTIONr_chiral_restr0.0740.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021900
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_it1.371.773724
X-RAY DIFFRACTIONr_mcbond_other1.3691.773722
X-RAY DIFFRACTIONr_mcangle_it2.0082.6474642
X-RAY DIFFRACTIONr_mcangle_other2.0082.6474643
X-RAY DIFFRACTIONr_scbond_it1.7991.9134049
X-RAY DIFFRACTIONr_scbond_other1.7991.9134050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6952.7965877
X-RAY DIFFRACTIONr_long_range_B_refined14.24524.07310059
X-RAY DIFFRACTIONr_long_range_B_other14.11523.6569927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.968 Å
RfactorNum. reflection% reflection
Rfree0.311 283 -
Rwork0.275 5187 -
obs--97.18 %

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