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- PDB-9fk4: The structure of glycosynthase XT6 (E265G mutant), the extracellu... -

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Basic information

Entry
Database: PDB / ID: 9fk4
TitleThe structure of glycosynthase XT6 (E265G mutant), the extracellular xylanase of G.proteiniphilus T-6 in complex with xylohexaose-F molecule
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: 1.9 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 xylohexaose-F molecule
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)45,07710
Polymers43,8011
Non-polymers1,2769
Water9,044502
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-211 kcal/mol
Surface area15240 Å2
Unit cell
Length a, b, c (Å)89.406, 61.648, 110.293
Angle α, β, γ (deg.)90.000, 105.467, 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-587-

HOH

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Components

#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
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-1-fluoro-D-xylopyranose


Type: oligosaccharide / Mass: 812.695 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]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.34 Å3/Da / Density % sol: 63.22 %
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: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→35.95 Å / Num. obs: 45734 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.11 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Rrim(I) all: 0.06 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2929 / CC1/2: 0.82 / Rpim(I) all: 0.29 / Rrim(I) all: 0.54

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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: 1.9→35.95 Å / SU ML: 0.1588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 2252 4.93 %
Rwork0.157 43466 -
obs0.1586 45718 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 63 502 3632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693236
X-RAY DIFFRACTIONf_angle_d0.84614401
X-RAY DIFFRACTIONf_chiral_restr0.0545469
X-RAY DIFFRACTIONf_plane_restr0.0056564
X-RAY DIFFRACTIONf_dihedral_angle_d8.2169464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.26431370.21872693X-RAY DIFFRACTION99.96
1.94-1.990.28951290.20622692X-RAY DIFFRACTION99.96
1.99-2.040.24691370.20582716X-RAY DIFFRACTION99.96
2.04-2.090.19471180.18262696X-RAY DIFFRACTION99.93
2.09-2.150.21491450.17462704X-RAY DIFFRACTION99.96
2.15-2.220.20241400.16752716X-RAY DIFFRACTION99.9
2.22-2.30.18251410.15662708X-RAY DIFFRACTION99.96
2.3-2.390.20191660.1642666X-RAY DIFFRACTION100
2.39-2.50.18341290.15452718X-RAY DIFFRACTION100
2.5-2.630.2231350.15922737X-RAY DIFFRACTION100
2.63-2.80.18481460.16352711X-RAY DIFFRACTION100
2.8-3.020.18651630.16612682X-RAY DIFFRACTION100
3.02-3.320.21031380.15592731X-RAY DIFFRACTION100
3.32-3.80.16041390.14272739X-RAY DIFFRACTION100
3.8-4.780.13311390.12522753X-RAY DIFFRACTION100
4.79-35.950.17951500.14212804X-RAY DIFFRACTION99.76

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