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- PDB-7d88: Crystal structure of a novel thermostable GH10 xylanase XynA -

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Basic information

Entry
Database: PDB / ID: 7d88
TitleCrystal structure of a novel thermostable GH10 xylanase XynA
ComponentsBeta-xylanase
KeywordsHYDROLASE / GH10 family / Thermostable / Bifunctional.
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34482019351 Å
AuthorsXie, W. / Yu, Q. / Wang, C.
CitationJournal: Biochemistry / Year: 2021
Title: Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities.
Authors: Xie, W. / Yu, Q. / Zhang, R. / Liu, Y. / Cao, R. / Wang, S. / Zhan, R. / Liu, Z. / Wang, K. / Wang, C.
History
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0033
Polymers49,9231
Non-polymers802
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.842, 109.842, 85.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

21A-666-

HOH

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Components

#1: Protein Beta-xylanase


Mass: 49922.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: KW1 / Gene: xyn10A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8ESF9, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 29% PEG 600 (w/v), 0.1 M CaCl2, 0.1 M MES pH 6.0 / PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→15.33 Å / Num. obs: 22405 / % possible obs: 99.35 % / Redundancy: 25.3 % / Biso Wilson estimate: 51.0611188386 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.031 / Rrim(I) all: 0.159 / Net I/σ(I): 30
Reflection shellResolution: 2.345→2.429 Å / Num. unique obs: 22405 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V0L

1v0l


Resolution: 2.34482019351→15.3263372188 Å / SU ML: 0.24062012499 / Cross valid method: FREE R-VALUE / σ(F): 1.37661057842 / Phase error: 24.5715151416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248285153375 1124 5.01718519841 %
Rwork0.214473386139 21279 -
obs0.216210592416 22403 99.8440146181 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.7565312641 Å2
Refinement stepCycle: LAST / Resolution: 2.34482019351→15.3263372188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 2 67 3044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008295851458423062
X-RAY DIFFRACTIONf_angle_d0.9652071653334155
X-RAY DIFFRACTIONf_chiral_restr0.0589742614023421
X-RAY DIFFRACTIONf_plane_restr0.00566542691731545
X-RAY DIFFRACTIONf_dihedral_angle_d10.20141627481770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.345-2.45110.2620507150471280.2127699905622599X-RAY DIFFRACTION98.9118607182
2.4511-2.57980.2736432910411310.2176252904572618X-RAY DIFFRACTION100
2.5798-2.74060.2694772916061510.219619770822604X-RAY DIFFRACTION100
2.7406-2.95080.2621306331041490.2107654858272619X-RAY DIFFRACTION100
2.9508-3.24520.2351894727671340.2098444750172657X-RAY DIFFRACTION100
3.2452-3.70890.2237923046771380.198451956142661X-RAY DIFFRACTION99.9642857143
3.7089-4.65110.2255841634291510.1981569186522690X-RAY DIFFRACTION99.9648135116
4.6511-15.3260.2728108947921420.2380906113052831X-RAY DIFFRACTION99.8991935484

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