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- PDB-9ul7: Improved thermostability of a GH3 glycosidase based on its X-ray ... -

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Basic information

Entry
Database: PDB / ID: 9ul7
TitleImproved thermostability of a GH3 glycosidase based on its X-ray crystal structure
Componentsbeta-glucosidase
KeywordsHYDROLASE / glycosidase / crystal / thermostability
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity
Similarity search - Function
: / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesClavibacter michiganensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDong, P.P. / Dong, P.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Improved thermostability of a GH3 glycosidase based on its X-ray crystal structure
Authors: Dong, P.P. / Dong, P.P.
History
DepositionApr 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)67,8351
Polymers67,8351
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.866, 104.617, 69.156
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-glucosidase


Mass: 67835.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavibacter michiganensis (bacteria) / Gene: bglX_1, BFL34_01020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A251YBN8, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 25% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 273645 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Net I/σ(I): 25.643
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 40984 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.559 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1936 4.76 %RANDOM
Rwork0.1895 ---
obs0.1917 40686 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 0 246 4877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074782
X-RAY DIFFRACTIONf_angle_d0.926507
X-RAY DIFFRACTIONf_dihedral_angle_d3.1892876
X-RAY DIFFRACTIONf_chiral_restr0.052707
X-RAY DIFFRACTIONf_plane_restr0.006885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.28831790.23492685X-RAY DIFFRACTION99
2.255-2.3160.29451490.21932749X-RAY DIFFRACTION100
2.316-2.38410.26481530.20252739X-RAY DIFFRACTION100
2.3841-2.4610.23971260.19342762X-RAY DIFFRACTION100
2.461-2.5490.26221080.19162792X-RAY DIFFRACTION100
2.549-2.6510.2551200.19722780X-RAY DIFFRACTION100
2.651-2.77160.25691520.19112730X-RAY DIFFRACTION100
2.7716-2.91760.24071750.19412736X-RAY DIFFRACTION100
2.9176-3.10030.22481280.19212776X-RAY DIFFRACTION100
3.1003-3.33950.28481110.18962803X-RAY DIFFRACTION100
3.3395-3.67530.24171500.18882760X-RAY DIFFRACTION100
3.6753-4.20630.20771700.18572750X-RAY DIFFRACTION100
4.2063-5.29640.27831080.17372820X-RAY DIFFRACTION100
5.2964-34.5580.17561070.19262868X-RAY DIFFRACTION100

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