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- PDB-9uj3: Improved thermostability of a GH10 xylanase based on its X-ray cr... -

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Basic information

Entry
Database: PDB / ID: 9uj3
TitleImproved thermostability of a GH10 xylanase based on its X-ray crystal structure
ComponentsBeta-xylanase
KeywordsHYDROLASE / xylanase / crystal / thermostability
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesMassilia sp. RBM26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 GH10 xylanase based on its X-ray crystal structure
Authors: Dong, P.P. / Dong, P.P.
History
DepositionApr 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)84,8162
Polymers84,8162
Non-polymers00
Water12,214678
1
A: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4081
Polymers42,4081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4081
Polymers42,4081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.077, 68.492, 90.538
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-xylanase


Mass: 42407.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Massilia sp. RBM26 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2I9J6, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion / Details: 0.16MCH3COONa,0.1MTris-HCl pH 8.5,28% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 49826 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.993 / Net I/σ(I): 18.722
Reflection shellResolution: 1.91→1.94 Å / Num. unique obs: 49826 / CC1/2: 0.919

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→33.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19305 2441 4.9 %RANDOM
Rwork0.15888 ---
obs0.16058 47353 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.346 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20.7 Å2
2---0.54 Å20 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.91→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 0 678 6212
LS refinement shellResolution: 1.913→1.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 144 -
Rwork0.175 3442 -
obs--96.76 %

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