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- PDB-9fk6: The structure of XT6 from G.proteiniphilus T-6: The E265G/N158D mutant -

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Basic information

Entry
Database: PDB / ID: 9fk6
TitleThe structure of XT6 from G.proteiniphilus T-6: The E265G/N158D 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: 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 XT6 from G.proteiniphilus T-6: The E265G/N158D 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)44,33010
Polymers43,8021
Non-polymers5299
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-216 kcal/mol
Surface area15760 Å2
Unit cell
Length a, b, c (Å)89.133, 61.874, 110.956
Angle α, β, γ (deg.)90.000, 105.372, 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-535-

HOH

21A-552-

HOH

31A-557-

HOH

41A-769-

HOH

51A-960-

HOH

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Components

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


Mass: 43801.566 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.: 7 / 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.: 520 / 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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 5K, 0.1M MES buffer at pH 6.5 and 0.02M 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: 1.95→39.82 Å / Num. obs: 42623 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.13 / Rrim(I) all: 0.3 / Net I/σ(I): 5.4
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2959 / CC1/2: 0.8 / Rpim(I) all: 0.35 / Rrim(I) all: 0.85

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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→36.55 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.4442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 2153 5.06 %
Rwork0.1774 40426 -
obs0.1791 42579 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 9 520 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663150
X-RAY DIFFRACTIONf_angle_d0.79464270
X-RAY DIFFRACTIONf_chiral_restr0.0532442
X-RAY DIFFRACTIONf_plane_restr0.0053556
X-RAY DIFFRACTIONf_dihedral_angle_d5.9873410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.29971180.21272684X-RAY DIFFRACTION99.89
2-2.050.24941660.20992668X-RAY DIFFRACTION99.93
2.05-2.10.25511420.18932671X-RAY DIFFRACTION99.96
2.1-2.160.2191220.18132698X-RAY DIFFRACTION100
2.16-2.230.20531440.18142702X-RAY DIFFRACTION99.96
2.23-2.310.1991410.17952686X-RAY DIFFRACTION99.89
2.31-2.40.23861290.18262679X-RAY DIFFRACTION99.82
2.4-2.510.23311680.17892670X-RAY DIFFRACTION100
2.51-2.650.20181400.18482700X-RAY DIFFRACTION99.82
2.65-2.810.19281630.17722661X-RAY DIFFRACTION99.86
2.81-3.030.23611300.18132695X-RAY DIFFRACTION99.86
3.03-3.330.21341500.17752703X-RAY DIFFRACTION99.96
3.33-3.820.19861570.16932708X-RAY DIFFRACTION99.86
3.82-4.810.17591260.15232734X-RAY DIFFRACTION99.76
4.81-36.550.19421570.17642767X-RAY DIFFRACTION99.35

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