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- PDB-22gt: a novel GH8 family xylanase BiXyn8A -

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Basic information

Entry
Database: PDB / ID: 22gt
Titlea novel GH8 family xylanase BiXyn8A
Componentscellulase
KeywordsHYDROLASE / GH8 family / endoxylanase
Function / homologyGlycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / cellulase / cellulase activity / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / cellulose catabolic process / cellulase
Function and homology information
Biological speciesBacteroides intestinalis DSM 17393 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.80000297631 Å
AuthorsWei, X. / Yun, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82274214 China
CitationJournal: Bioresour Technol / Year: 2026
Title: Biochemical and structural characterization of a novel glycoside hydrolase family 8 endoxylanase with broad-spectrum xylooligosaccharide production.
Authors: Liu, Y. / Xie, W. / Zhang, Y. / Liang, S. / Wang, S. / Zhan, R. / Wang, C. / Wang, K.
History
DepositionJan 10, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cellulase
B: cellulase


Theoretical massNumber of molelcules
Total (without water)94,4992
Polymers94,4992
Non-polymers00
Water6,846380
1
A: cellulase


Theoretical massNumber of molelcules
Total (without water)47,2501
Polymers47,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cellulase


Theoretical massNumber of molelcules
Total (without water)47,2501
Polymers47,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.600, 94.520, 103.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein cellulase


Mass: 47249.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria)
Gene: BACINT_04210 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CES9, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→25.01 Å / Num. obs: 386257 / % possible obs: 98.98 % / Redundancy: 4.8 % / Biso Wilson estimate: 19.7758750919 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 14.88
Reflection shellResolution: 1.8→10 Å / Mean I/σ(I) obs: 14.88 / Num. unique obs: 77988 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
AUTOMARdata reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.80000297631→25.0082581824 Å / SU ML: 0.192869828307 / Cross valid method: FREE R-VALUE / σ(F): 1.3493385646 / Phase error: 21.6974524398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213436026995 3896 5.003210479 %
Rwork0.182194884673 73974 -
obs0.183776102323 77870 99.038485997 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.2505307492 Å2
Refinement stepCycle: LAST / Resolution: 1.80000297631→25.0082581824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 0 380 6638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006766307311286454
X-RAY DIFFRACTIONf_angle_d0.8495656632638735
X-RAY DIFFRACTIONf_chiral_restr0.0525474078971850
X-RAY DIFFRACTIONf_plane_restr0.005247392416711121
X-RAY DIFFRACTIONf_dihedral_angle_d5.960646686153722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.82190.3189534160361250.245957187282569X-RAY DIFFRACTION96.2486602358
1.8219-1.8450.2973280274681430.23543093392550X-RAY DIFFRACTION97.8916757543
1.845-1.86930.2460040224961260.229497790052584X-RAY DIFFRACTION97.6576576577
1.8693-1.89490.2360630148511340.2177587468982572X-RAY DIFFRACTION97.7248104009
1.8949-1.92190.2393497579011420.2102122127372576X-RAY DIFFRACTION98.3001808318
1.9219-1.95060.260830781691360.2155079102142607X-RAY DIFFRACTION98.2449856734
1.9506-1.98110.274784531251240.221992223492613X-RAY DIFFRACTION98.4532374101
1.9811-2.01350.2712842541471330.2149357926242593X-RAY DIFFRACTION98.4470928133
2.0135-2.04820.2690212179261470.1995835379072585X-RAY DIFFRACTION98.9855072464
2.0482-2.08550.2279490229181340.1943143512622637X-RAY DIFFRACTION98.8583660364
2.0855-2.12560.2049602291831470.1995259571322611X-RAY DIFFRACTION99.2086330935
2.1256-2.16890.2640335270891250.1911256440142638X-RAY DIFFRACTION99.2456896552
2.1689-2.21610.2703118108021420.1943501107652624X-RAY DIFFRACTION99.4248741912
2.2161-2.26760.2254502483131370.1887895470562629X-RAY DIFFRACTION99.4606256742
2.2676-2.32420.238633162481300.1844315477732678X-RAY DIFFRACTION99.8577524893
2.3242-2.3870.2332670830881240.1977028001012645X-RAY DIFFRACTION99.6760259179
2.387-2.45720.2333536106781570.1900174230832641X-RAY DIFFRACTION99.8216196932
2.4572-2.53650.2178847103121360.1951941266482665X-RAY DIFFRACTION99.6442547136
2.5365-2.6270.2203921042041400.1894896546142639X-RAY DIFFRACTION99.605734767
2.627-2.73210.2436714008491400.1945676735852661X-RAY DIFFRACTION99.6088193457
2.7321-2.85630.2388726936411380.1879927960172663X-RAY DIFFRACTION99.5734091717
2.8563-3.00660.2083493541971410.1951235747632659X-RAY DIFFRACTION99.4318181818
3.0066-3.19460.2219290611611400.1897024073582678X-RAY DIFFRACTION99.5759717314
3.1946-3.44070.1981972070181520.1829764894612685X-RAY DIFFRACTION99.8943661972
3.4407-3.78590.187446530221510.1624401652532670X-RAY DIFFRACTION99.7877608773
3.7859-4.33130.1822338573861480.1446987972452731X-RAY DIFFRACTION99.826629681
4.3313-5.44770.1496035782841370.141668195352746X-RAY DIFFRACTION99.8614478698
5.4477-250.1709491351571670.1611343031272825X-RAY DIFFRACTION98.8437396762

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