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- PDB-9fk7: The structure of XT6 from G.proteiniphilus T-6: The E265G/N158E mutant -

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Basic information

Entry
Database: PDB / ID: 9fk7
TitleThe structure of XT6 from G.proteiniphilus T-6: The E265G/N158E mutant
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 XT6 from G.proteiniphilus T-6: The E265G/N158E mutant
Authors: Hadad, N. / Chmelnik, O. / Dessau, M. / Shoham, Y. / Shoham, G.
History
DepositionJun 2, 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: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,53911
Polymers43,8161
Non-polymers72310
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.000, 61.915, 110.912
Angle α, β, γ (deg.)90.000, 105.131, 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-568-

HOH

21A-574-

HOH

31A-649-

HOH

41A-880-

HOH

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Components

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


Mass: 43815.594 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 5K, 0.1M MES buffer at pH 6.5 and 0.01M Zinc chloride

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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: Sep 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→35.89 Å / Num. obs: 29762 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 16.58 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.05 / Rrim(I) all: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2566 / CC1/2: 0.8 / Rpim(I) all: 0.25 / Rrim(I) all: 0.46

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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→35.89 Å / SU ML: 0.1691 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 1486 4.99 %
Rwork0.157 28269 -
obs0.159 29755 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 22 429 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693163
X-RAY DIFFRACTIONf_angle_d0.82424282
X-RAY DIFFRACTIONf_chiral_restr0.0519442
X-RAY DIFFRACTIONf_plane_restr0.0053556
X-RAY DIFFRACTIONf_dihedral_angle_d6.5304417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.24261360.1922538X-RAY DIFFRACTION99.44
2.27-2.350.24721380.18042584X-RAY DIFFRACTION99.93
2.35-2.450.22651200.17632547X-RAY DIFFRACTION100
2.45-2.560.24391290.16782546X-RAY DIFFRACTION99.96
2.56-2.690.22251220.17222568X-RAY DIFFRACTION99.96
2.69-2.860.19251290.16812589X-RAY DIFFRACTION100
2.86-3.080.23021510.17432533X-RAY DIFFRACTION100
3.08-3.390.19561460.16392565X-RAY DIFFRACTION100
3.39-3.880.20551290.14662588X-RAY DIFFRACTION100
3.88-4.890.13411420.12342577X-RAY DIFFRACTION100
4.89-35.890.17681440.13752634X-RAY DIFFRACTION99.57

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