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- PDB-21xq: a novel GH8 family endoxylanase BgXyn8A -

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Basic information

Entry
Database: PDB / ID: 21xq
Titlea novel GH8 family endoxylanase BgXyn8A
ComponentsGlycosyl hydrolase family 8
KeywordsHYDROLASE / endoxylanase GH8
Function / homologyGlycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / Glycosyl hydrolase family 8
Function and homology information
Biological speciesBacillus glycinifermentans (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.20002441176 Å
AuthorsXie, W. / Liu, Y.
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 3, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 8


Theoretical massNumber of molelcules
Total (without water)45,1011
Polymers45,1011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.935, 104.935, 76.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Glycosyl hydrolase family 8


Mass: 45101.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus glycinifermentans (bacteria) / Gene: AB447_216495, P8828_09935 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J6ECL7
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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, sodium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54184 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→21 Å / Num. obs: 24887 / % possible obs: 99.81 % / Redundancy: 8.9 % / Biso Wilson estimate: 17.1587132968 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 35.41
Reflection shellResolution: 2.2→20.2 Å / Rmerge(I) obs: 0.037 / Num. unique obs: 24886

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
autoPROCdata processing
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.20002441176→20.1 Å / SU ML: 0.251424136734 / Cross valid method: FREE R-VALUE / σ(F): 1.35221060613 / Phase error: 21.5979681526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225091379747 1235 4.96243018443 %
Rwork0.19387416799 23652 -
obs0.195481698924 24887 99.9879469667 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.225084566 Å2
Refinement stepCycle: LAST / Resolution: 2.20002441176→20.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 0 0 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007305700675473261
X-RAY DIFFRACTIONf_angle_d0.8285383432054407
X-RAY DIFFRACTIONf_chiral_restr0.0455592062975443
X-RAY DIFFRACTIONf_plane_restr0.00484052297627574
X-RAY DIFFRACTIONf_dihedral_angle_d6.515200841281896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.2880.2965865424881410.2200911642082578X-RAY DIFFRACTION100
2.288-2.3920.2706839979531280.2169859945882608X-RAY DIFFRACTION100
2.392-2.51780.2988375283541360.2213462442892585X-RAY DIFFRACTION100
2.5178-2.67530.2790315856661450.2116471871562594X-RAY DIFFRACTION100
2.6753-2.88130.223748894871420.2074790597082616X-RAY DIFFRACTION100
2.8813-3.17020.2577297841631600.2158413242082609X-RAY DIFFRACTION100
3.1702-3.62660.2331907233221230.196191873582647X-RAY DIFFRACTION100
3.6266-4.56040.1544959298231540.1585266193422635X-RAY DIFFRACTION100
4.5604-200.1717346427181060.1692972723742780X-RAY DIFFRACTION99.8961578401

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