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- PDB-8xy0: Activity-stability trade-off observed in variants at position 315... -

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Basic information

Entry
Database: PDB / ID: 8xy0
TitleActivity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / GH10 / Alkaliphily / Alkaline resistance / Thermostability / Xylanase
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. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus sp. TAR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakamura, T. / Takita, T. / Mizutani, K. / Mikami, B. / Nakamura, S. / Yasukawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)30397559 Japan
CitationJournal: Sci Rep / Year: 2024
Title: Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Authors: Nakamura, T. / Takita, T. / Kuwata, K. / Mizutani, K. / Mikami, B. / Nakamura, S. / Yasukawa, K.
History
DepositionJan 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4175
Polymers42,0581
Non-polymers3584
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.179, 41.783, 80.873
Angle α, β, γ (deg.)90.000, 90.520, 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
11A-547-

HOH

21A-783-

HOH

31A-797-

HOH

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Components

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


Mass: 42058.156 Da / Num. of mol.: 1 / Mutation: T315Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. TAR1 (bacteria) / Gene: xynA, BH2120 / Plasmid: pET-21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07528, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.32 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9 / Details: 0.2 M ammonium iodide, 26% w/v PEG4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26490 / % possible obs: 94.4 % / Redundancy: 3.87 % / Biso Wilson estimate: 22.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.078 / Net I/σ(I): 13.05
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 3206 / CC1/2: 0.829 / Rrim(I) all: 0.434 / % possible all: 71.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.27 Å / SU ML: 0.2001 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2201 1325 5 %
Rwork0.1705 25161 -
obs0.173 26486 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 22 336 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793050
X-RAY DIFFRACTIONf_angle_d0.94484147
X-RAY DIFFRACTIONf_chiral_restr0.0597421
X-RAY DIFFRACTIONf_plane_restr0.0077551
X-RAY DIFFRACTIONf_dihedral_angle_d6.569411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.29421040.23971966X-RAY DIFFRACTION67.51
1.98-2.070.24351290.19332462X-RAY DIFFRACTION83.93
2.07-2.170.2351530.17342898X-RAY DIFFRACTION98.55
2.17-2.310.21311540.19382927X-RAY DIFFRACTION99.87
2.31-2.490.24811560.17722965X-RAY DIFFRACTION99.97
2.49-2.740.22831550.18052950X-RAY DIFFRACTION99.97
2.74-3.140.23781560.1842960X-RAY DIFFRACTION99.87
3.14-3.950.21391560.1552974X-RAY DIFFRACTION99.75
3.95-44.270.18771620.15043059X-RAY DIFFRACTION99.54

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