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- PDB-9fk1: The structure of glycosynthase XT6 (E265G mutant), the extracellu... -

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Basic information

Entry
Database: PDB / ID: 9fk1
TitleThe structure of glycosynthase XT6 (E265G mutant), the extracellular xylanase of G.proteiniphilus T-6
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: 1.95 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
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)44,39511
Polymers43,8011
Non-polymers59410
Water9,710539
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-248 kcal/mol
Surface area15810 Å2
Unit cell
Length a, b, c (Å)88.980, 61.900, 111.322
Angle α, β, γ (deg.)90.000, 104.983, 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-549-

HOH

21A-988-

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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 63.56 %
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 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→39.83 Å / Num. obs: 42630 / % possible obs: 99.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2952 / CC1/2: 0.59 / Rpim(I) all: 0.45 / Rrim(I) all: 0.93

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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: 1.95→39.83 Å / SU ML: 0.1938 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2053 2167 5.08 %
Rwork0.1631 40453 -
obs0.1653 42620 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 10 539 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683159
X-RAY DIFFRACTIONf_angle_d0.79224283
X-RAY DIFFRACTIONf_chiral_restr0.0521443
X-RAY DIFFRACTIONf_plane_restr0.0052558
X-RAY DIFFRACTIONf_dihedral_angle_d6.0418413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.31951260.25122661X-RAY DIFFRACTION97.82
2-2.050.27421610.24392628X-RAY DIFFRACTION98.45
2.05-2.10.26321430.21172641X-RAY DIFFRACTION98.72
2.1-2.160.26471250.19622715X-RAY DIFFRACTION99.09
2.16-2.230.20421470.18682672X-RAY DIFFRACTION99.44
2.23-2.310.21251390.17482705X-RAY DIFFRACTION99.58
2.31-2.40.24641300.17922681X-RAY DIFFRACTION99.82
2.4-2.510.24181660.17012679X-RAY DIFFRACTION99.96
2.51-2.650.21521390.16952711X-RAY DIFFRACTION100
2.65-2.810.21711660.16182677X-RAY DIFFRACTION99.96
2.81-3.030.22021340.16032717X-RAY DIFFRACTION100
3.03-3.330.19881480.1532702X-RAY DIFFRACTION100
3.33-3.820.17391570.14182734X-RAY DIFFRACTION100
3.82-4.810.15911270.12232740X-RAY DIFFRACTION100
4.81-39.830.15331590.14192790X-RAY DIFFRACTION99.59

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