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

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Basic information

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


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / 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: 2.6 Å
AuthorsDong, P.P. / Lu, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Other governmentZhejiang Provincial Natural Science Foundation of China LQN25C050002 China
CitationJournal: To Be Published
Title: Improved thermostability of a GH10 xylanase based on its X-ray crystal structure
Authors: Dong, P.P. / Lu, P.
History
DepositionApr 28, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,9792
Polymers78,9792
Non-polymers00
Water1,45981
1
A: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)39,4901
Polymers39,4901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)39,4901
Polymers39,4901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.350, 69.300, 91.080
Angle α, β, γ (deg.)90.000, 91.914, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-xylanase


Mass: 39489.535 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.: 81 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.1MBis-TrispH 7.0,25%(W/V) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→46.694 Å / Num. obs: 39554 / % possible obs: 98.7 % / Redundancy: 3.43 % / CC1/2: 0.961 / Net I/σ(I): 5.64
Reflection shellResolution: 2.6→2.76 Å / Num. unique obs: 6333 / CC1/2: 0.665

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.694 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.832 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.418
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 1023 4.972 %RANDOM
Rwork0.242 19552 --
all0.245 ---
obs-20575 99.835 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å20 Å20.027 Å2
2---0.004 Å20 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 0 81 5629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.6-2.6670.431720.32814440.33315260.870.91999.34470.321
2.667-2.740.385550.32813850.3314400.90.9251000.313
2.74-2.8190.393730.32913760.33314490.8960.9231000.306
2.819-2.9050.324710.31213070.31313790.9240.9399.92750.286
2.905-30.367630.30712680.3113310.9020.9341000.278
3-3.1050.32490.28812680.28913190.9380.94199.84840.267
3.105-3.2220.32760.28111590.28312350.9190.9441000.247
3.222-3.3530.271570.27212000.27212590.9560.95199.84110.25
3.353-3.5010.318610.24310820.24711430.9390.9611000.228
3.501-3.6710.288540.23110690.23411230.9550.9661000.209
3.671-3.8680.238510.22610120.22610630.9660.971000.211
3.868-4.1010.26610.29390.20310020.9560.97599.80040.186
4.101-4.3820.284670.1938950.29620.9560.9771000.179
4.382-4.7290.25490.1868240.1898730.9650.9791000.174
4.729-5.1750.185450.1887720.1888170.9770.981000.178
5.175-5.7770.301330.2087190.2127520.9450.9731000.192
5.777-6.6540.228380.2276220.2276600.9750.971000.21
6.654-8.1080.216150.1965380.1975530.9740.9751000.19
8.108-11.2980.215200.1644300.1664500.9730.9831000.168
11.298-46.6940.602130.2682430.2822700.7840.95394.81480.279

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