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- PDB-7f3a: Arabidopsis thaliana GH1 beta-glucosidase AtBGlu42 -

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Basic information

Entry
Database: PDB / ID: 7f3a
TitleArabidopsis thaliana GH1 beta-glucosidase AtBGlu42
ComponentsBeta-glucosidase 42
KeywordsHYDROLASE / glycoside hydrolase family 1 / beta-glucosidase
Function / homology
Function and homology information


induced systemic resistance, ethylene mediated signaling pathway / positive regulation of defense response / response to iron ion starvation / : / secondary metabolic process / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / response to bacterium / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHorikoshi, S. / Saburi, W. / Yu, J. / Yao, M.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2022
Title: Substrate specificity of glycoside hydrolase family 1 beta-glucosidase AtBGlu42 from Arabidopsis thaliana and its molecular mechanism.
Authors: Horikoshi, S. / Saburi, W. / Yu, J. / Matsuura, H. / Cairns, J.R.K. / Yao, M. / Mori, H.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase 42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5995
Polymers56,2311
Non-polymers3684
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.690, 93.106, 60.931
Angle α, β, γ (deg.)90.000, 102.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-glucosidase 42 / AtBGLU42


Mass: 56230.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BGLU42, At5g36890, MLF18.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIW4, beta-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 9% (w/v) PEG 8000, 0.1 M calcium acetate, 0.05 M sodium cacodylate buffer (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→46.553 Å / Num. obs: 53471 / % possible obs: 99.97 % / Redundancy: 6.76 % / CC1/2: 0.999 / Rrim(I) all: 0.081 / Net I/σ(I): 15.14
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.87 % / Mean I/σ(I) obs: 2 / Num. unique obs: 8612 / CC1/2: 0.783 / Rrim(I) all: 0.849 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gno

3gno


Resolution: 1.7→46.553 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 1999 3.74 %
Rwork0.1601 51472 -
obs0.1609 53471 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.76 Å2 / Biso mean: 25.9446 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 1.7→46.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 24 402 4291
Biso mean--30.41 34.59 -
Num. residues----477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error
1.7-1.74250.30721420.257436760
1.7425-1.78960.25371440.221536720
1.7896-1.84230.24221410.202436410
1.8423-1.90180.24111430.190736710
1.9018-1.96970.21571410.183336510
1.9697-2.04860.22211420.182836660
2.0486-2.14180.20581430.161636820
2.1418-2.25480.17751430.158836700
2.2548-2.3960.20611430.166736750
2.396-2.5810.18741420.160436700
2.581-2.84070.19541420.164236640
2.8407-3.25170.19211440.153736840
3.2517-4.09640.14881440.136737140
4.0964-46.5530.13231450.14653736

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