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- PDB-9fkk: The structure of glycosynthase IXT6 (E241G mutant), the intracell... -

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Basic information

Entry
Database: PDB / ID: 9fkk
TitleThe structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6 in complex with xylobiose-F and xylotetraose-F molecules
ComponentsBeta-xylanase
KeywordsHYDROLASE / IXT6 / glycosynthase / Geobacillus proteiniphilus T-6 / Geobacillus stearothermophilus
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesGeobacillus proteiniphilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHadad, N. / Chmelnik, O. / Dessau, M. / Shoham, Y. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6 in complex with xylobiose-F and xylotetraose-F molecules
Authors: Hadad, N. / Chmelnik, O. / Dessau, M. / Shoham, Y. / Shoham, G.
History
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1015
Polymers77,2462
Non-polymers8563
Water8,755486
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1712
Polymers38,6231
Non-polymers5481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9303
Polymers38,6231
Non-polymers3072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.924, 81.458, 79.620
Angle α, β, γ (deg.)90.000, 91.654, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Beta-xylanase


Mass: 38622.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus proteiniphilus (bacteria) / Gene: xynA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09LY9, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-1-fluoro-D-xylopyranose


Type: oligosaccharide / Mass: 548.465 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
[][<C5O3F1>]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-4)-1-fluoro-D-xylopyranose


Type: oligosaccharide / Mass: 284.236 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
[][<C5O3F1>]{[(1+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Sodium acetate and 0.1M Sodium cacodylate buffer at pH 6.5.

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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: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→40.73 Å / Num. obs: 42632 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.56 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.06 / Rrim(I) all: 0.13 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4446 / CC1/2: 0.75 / Rpim(I) all: 0.37 / Rrim(I) all: 0.71

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.73 Å / SU ML: 0.2637 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 2149 5.05 %
Rwork0.1674 40436 -
obs0.1697 42585 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5420 0 57 486 5963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795641
X-RAY DIFFRACTIONf_angle_d0.95167655
X-RAY DIFFRACTIONf_chiral_restr0.0567811
X-RAY DIFFRACTIONf_plane_restr0.0055989
X-RAY DIFFRACTIONf_dihedral_angle_d8.3627768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.32141280.24532662X-RAY DIFFRACTION99.61
2.46-2.520.29131250.22442679X-RAY DIFFRACTION99.82
2.52-2.590.27351430.22222695X-RAY DIFFRACTION99.86
2.59-2.660.31831400.21492692X-RAY DIFFRACTION99.79
2.66-2.750.23731450.2072682X-RAY DIFFRACTION99.93
2.75-2.850.25971500.19852681X-RAY DIFFRACTION99.93
2.85-2.960.24571310.20682679X-RAY DIFFRACTION100
2.96-3.090.26371670.20352663X-RAY DIFFRACTION99.93
3.09-3.260.25251380.18822703X-RAY DIFFRACTION100
3.26-3.460.25111370.17322707X-RAY DIFFRACTION99.96
3.46-3.730.20061400.14562699X-RAY DIFFRACTION100
3.73-4.10.15531490.13052690X-RAY DIFFRACTION99.86
4.1-4.70.15291540.11622724X-RAY DIFFRACTION100
4.7-5.910.15371520.13342703X-RAY DIFFRACTION100
5.91-40.730.16331500.1472777X-RAY DIFFRACTION99.69

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