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- PDB-9fk3: The structure of glycosynthase XT6 (E265G mutant), the extracellu... -

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Basic information

Entry
Database: PDB / ID: 9fk3
TitleThe structure of glycosynthase XT6 (E265G mutant), the extracellular xylanase of G.proteiniphilus T-6 in complex with xylobiose-F and xylotetraose-F molecules
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / XT6 / glycosynthase / Geobacillus proteiniphilus T-6
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / 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
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesGeobacillus proteiniphilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 XT6 (E265G mutant), the extracellular 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 1, 2024Deposition site: PDBE / Processing site: PDBE
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: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,09711
Polymers43,8011
Non-polymers1,29610
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-203 kcal/mol
Surface area15660 Å2
Unit cell
Length a, b, c (Å)89.592, 61.901, 110.647
Angle α, β, γ (deg.)90.000, 105.252, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-611-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endo-1,4-beta-xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase


Mass: 43800.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus proteiniphilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P40943, endo-1,4-beta-xylanase

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Sugars , 2 types, 2 molecules

#2: 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
#3: 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

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Non-polymers , 3 types, 409 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.01M Zinc chloride, 17% PEG 5000, and 0.1M MES 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: Oct 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→34.1 Å / Num. obs: 29862 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.06 / Rrim(I) all: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2589 / CC1/2: 0.79 / Rpim(I) all: 0.31 / Rrim(I) all: 0.56

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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: 2.2→34.1 Å / SU ML: 0.2002 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 1482 4.96 %
Rwork0.1545 28377 -
obs0.1567 29859 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 8 401 3532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733210
X-RAY DIFFRACTIONf_angle_d0.84814358
X-RAY DIFFRACTIONf_chiral_restr0.0533464
X-RAY DIFFRACTIONf_plane_restr0.0057556
X-RAY DIFFRACTIONf_dihedral_angle_d7.506454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.27071370.20362554X-RAY DIFFRACTION99.89
2.27-2.350.2691320.18772583X-RAY DIFFRACTION100
2.35-2.450.21681540.1832540X-RAY DIFFRACTION100
2.45-2.560.25911400.17052562X-RAY DIFFRACTION99.96
2.56-2.690.21281440.17222542X-RAY DIFFRACTION100
2.69-2.860.21251260.16752588X-RAY DIFFRACTION99.96
2.86-3.080.22831220.16682585X-RAY DIFFRACTION100
3.08-3.390.20091160.1582582X-RAY DIFFRACTION99.96
3.39-3.880.18581530.13962576X-RAY DIFFRACTION99.89
3.88-4.890.16431300.12142598X-RAY DIFFRACTION99.89
4.89-34.10.13941280.1362667X-RAY DIFFRACTION99.86

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