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- PDB-7d89: Crystal structure of an inactivated double mutant (E182AE280A) of... -

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Basic information

Entry
Database: PDB / ID: 7d89
TitleCrystal structure of an inactivated double mutant (E182AE280A) of a novel thermostable GH10 xylanase XynA
ComponentsBeta-xylanase
KeywordsHYDROLASE / GH10 family / Thermostable / Inactivated / mutant
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: 2.89384086853 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)49,8873
Polymers49,8071
Non-polymers802
Water362
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 area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.193, 110.193, 84.983
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

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Components

#1: Protein Beta-xylanase


Mass: 49806.918 Da / Num. of mol.: 1 / Mutation: E182A, E280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: KW1 / Gene: xyn10A / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 2 / 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: 52.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 24% PEG 600, 0.1M CaCl2, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→49.28 Å / Num. obs: 12123 / % possible obs: 99.56 % / Redundancy: 25.5 % / Biso Wilson estimate: 66.2367949314 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.021 / Rrim(I) all: 0.108 / Net I/σ(I): 34
Reflection shellResolution: 2.894→2.997 Å / Rmerge(I) obs: 0.108 / Num. unique obs: 12123 / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.108

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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: 2.89384086853→49.2798077289 Å / SU ML: 0.397124008712 / Cross valid method: FREE R-VALUE / σ(F): 1.37753762711 / Phase error: 28.1305524779
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.27908203961 596 4.91627484946 %
Rwork0.232358677675 11527 -
obs0.234647402838 12123 99.6056199162 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.640519927 Å2
Refinement stepCycle: LAST / Resolution: 2.89384086853→49.2798077289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 2 2 2863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009233588767912945
X-RAY DIFFRACTIONf_angle_d1.061545462023999
X-RAY DIFFRACTIONf_chiral_restr0.0586101665999404
X-RAY DIFFRACTIONf_plane_restr0.00586163999793524
X-RAY DIFFRACTIONf_dihedral_angle_d10.42491411411690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.1850.3575554743911340.2415149960442771X-RAY DIFFRACTION98.5413839891
3.185-3.64580.2560388734571480.2236638135852844X-RAY DIFFRACTION100
3.6458-4.59280.2674155956771690.2060018570362862X-RAY DIFFRACTION99.9670184697
4.5928-6.70.2806041522591450.2540271031243050X-RAY DIFFRACTION99.9061913696

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