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- PDB-8i0x: Beta-Xylosidase JB13GH39P28 showing salt/ethanol/trypsin toleranc... -

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Basic information

Entry
Database: PDB / ID: 8i0x
TitleBeta-Xylosidase JB13GH39P28 showing salt/ethanol/trypsin tolerance, low-pH/low-Temperature activity, and transformation of notoginsenosides
ComponentsGlycoside hydrolase family 39 beta-xylosidase
KeywordsHYDROLASE / salt tolerance / transformation of notoginsenosides
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / : / Glycosyl hydrolases family 39 / : / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycoside hydrolase family 39 beta-xylosidase
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, J.P. / Cao, L.J. / Lin, M.Y. / Zhang, R. / Huang, Z.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: beta-Xylosidase JB13GH39P28(D41G)showing salt/ethanol/trypsin tolerance and transformation of notoginsenosides
Authors: Cao, L.J. / Lin, M.Y. / Zhang, R. / Huang, Z.X. / Zhou, J.P.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycoside hydrolase family 39 beta-xylosidase
A: Glycoside hydrolase family 39 beta-xylosidase


Theoretical massNumber of molelcules
Total (without water)116,6612
Polymers116,6612
Non-polymers00
Water16,430912
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.403, 62.627, 140.117
Angle α, β, γ (deg.)90.000, 91.419, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycoside hydrolase family 39 beta-xylosidase


Mass: 58330.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A3G6ZHU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 3350,100 mM BIS-TRIS propane pH 8.5, 20.00 mM Sodium Potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 17, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.999→32.64 Å / Num. obs: 75588 / % possible obs: 97.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.18 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rpim(I) all: 0.1385 / Rrim(I) all: 0.3529 / Net I/σ(I): 6.37
Reflection shellResolution: 1.999→2.071 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 7109 / CC1/2: 0.515 / CC star: 0.825 / % possible all: 94.51

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
DIALS3.7.2data reduction
DIALS3.7.2data scaling
PHENIX1.15.1_3469phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.64 Å / SU ML: 0.1881 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.6381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 3708 5 %
Rwork0.1687 70524 -
obs0.1707 74232 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.78 Å2
Refinement stepCycle: LAST / Resolution: 2→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7902 0 0 912 8814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00458142
X-RAY DIFFRACTIONf_angle_d0.759411116
X-RAY DIFFRACTIONf_chiral_restr0.04881178
X-RAY DIFFRACTIONf_plane_restr0.00491456
X-RAY DIFFRACTIONf_dihedral_angle_d11.38944778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.31261160.252569X-RAY DIFFRACTION93.88
2.03-2.050.25831330.232590X-RAY DIFFRACTION94.78
2.05-2.080.25761330.22922657X-RAY DIFFRACTION95.19
2.08-2.110.27741210.21622621X-RAY DIFFRACTION96.18
2.11-2.150.25961680.20842692X-RAY DIFFRACTION97.31
2.15-2.180.23021570.2052634X-RAY DIFFRACTION97.93
2.18-2.220.22311520.20032729X-RAY DIFFRACTION98.09
2.22-2.260.25251520.19822696X-RAY DIFFRACTION98.85
2.26-2.30.24911460.19782793X-RAY DIFFRACTION99.53
2.3-2.350.23261210.19242721X-RAY DIFFRACTION99.47
2.35-2.40.20091270.18652740X-RAY DIFFRACTION98.83
2.4-2.460.2611650.18282696X-RAY DIFFRACTION99.51
2.46-2.520.25211750.1872742X-RAY DIFFRACTION99.52
2.52-2.590.19871840.18142719X-RAY DIFFRACTION99.79
2.59-2.660.23761120.18262777X-RAY DIFFRACTION99.48
2.66-2.750.2151500.17982733X-RAY DIFFRACTION99.28
2.75-2.850.25441760.18342724X-RAY DIFFRACTION99.38
2.85-2.960.22091670.18162718X-RAY DIFFRACTION99.62
2.96-3.10.2331550.17722760X-RAY DIFFRACTION99.35
3.1-3.260.22521130.16782787X-RAY DIFFRACTION99.01
3.26-3.460.1771090.16272771X-RAY DIFFRACTION98.73
3.46-3.730.20471230.15182739X-RAY DIFFRACTION97.98
3.73-4.10.14941120.12942759X-RAY DIFFRACTION97.49
4.1-4.70.16321460.11782745X-RAY DIFFRACTION98.03
4.7-5.910.16411490.13592735X-RAY DIFFRACTION97.17
5.91-7.10.16681460.14862677X-RAY DIFFRACTION92.86

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