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- PDB-9fkh: The structure of glycosynthase IXT6 (E241G mutant), the intracell... -

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Basic information

Entry
Database: PDB / ID: 9fkh
TitleThe structure of glycosynthase IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6
ComponentsBeta-xylanase
KeywordsHYDROLASE / IXT6 / glycosynthase / Geobacillus proteiniphilus T-6 / Geobacillus stearothermophilus
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
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
Biological speciesGeobacillus proteiniphilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 IXT6 (E241G mutant), the intracellular xylanase of G.proteiniphilus T-6
Authors: Hadad, N. / Chmelnik, O. / Dessau, M. / Shoham, Y. / Shoham, G.
History
DepositionJun 3, 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: Beta-xylanase
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)77,2462
Polymers77,2462
Non-polymers00
Water9,746541
1
A: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)38,6231
Polymers38,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)38,6231
Polymers38,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.317, 80.218, 78.961
Angle α, β, γ (deg.)90.000, 91.883, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-615-

HOH

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Components

#1: Protein Beta-xylanase


Mass: 38622.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus proteiniphilus (bacteria) / Gene: xynA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09LY9, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Sodium acetate and 0.1M Sodium cacodylate 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 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→40.11 Å / Num. obs: 46869 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4495 / CC1/2: 0.66 / Rpim(I) all: 0.4 / Rrim(I) all: 0.63

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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: 2.3→40.11 Å / SU ML: 0.2507 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.5636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2082 2258 4.82 %
Rwork0.1706 44590 -
obs0.1724 46848 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 0 541 5953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785624
X-RAY DIFFRACTIONf_angle_d0.89837630
X-RAY DIFFRACTIONf_chiral_restr0.055793
X-RAY DIFFRACTIONf_plane_restr0.00571000
X-RAY DIFFRACTIONf_dihedral_angle_d6.1026735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.30011560.25212703X-RAY DIFFRACTION98.11
2.35-2.40.28981380.25172747X-RAY DIFFRACTION98.5
2.4-2.460.27121240.24472753X-RAY DIFFRACTION98.9
2.46-2.530.30161300.23012794X-RAY DIFFRACTION99.52
2.53-2.610.30581090.23182795X-RAY DIFFRACTION99.66
2.61-2.690.26131400.22122772X-RAY DIFFRACTION99.69
2.69-2.790.25881420.20532772X-RAY DIFFRACTION99.59
2.79-2.90.24741500.20192773X-RAY DIFFRACTION99.59
2.9-3.030.28251380.1992827X-RAY DIFFRACTION99.76
3.03-3.190.21541330.18852785X-RAY DIFFRACTION99.76
3.19-3.390.19931650.16712751X-RAY DIFFRACTION99.79
3.39-3.650.17651470.14582810X-RAY DIFFRACTION99.76
3.65-4.020.16521340.12532822X-RAY DIFFRACTION99.8
4.02-4.60.15861520.1212781X-RAY DIFFRACTION99.9
4.6-5.790.17051680.13452802X-RAY DIFFRACTION99.9
5.79-40.110.17031320.1572903X-RAY DIFFRACTION99.48

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