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- PDB-8he1: The structure of chitin deacetylase Pst_13661 from Puccinia strii... -

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Basic information

Entry
Database: PDB / ID: 8he1
TitleThe structure of chitin deacetylase Pst_13661 from Puccinia striiformis f. sp. tritici
ComponentsChitin deacetylase
KeywordsHYDROLASE / Chitin deacetylase / Plant pathogenic fungi / Virulence factor
Function / homology
Function and homology information


chitin deacetylase activity / side of membrane / cell wall organization / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
BENZHYDROXAMIC ACID / NodB homology domain-containing protein
Similarity search - Component
Biological speciesPuccinia striiformis f. sp. tritici (stripe rust fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLiu, L. / Li, Y.C. / Zhou, Y. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32001938 China
CitationJournal: Nat Commun / Year: 2023
Title: Inhibition of chitin deacetylases to attenuate plant fungal diseases.
Authors: Liu, L. / Xia, Y. / Li, Y. / Zhou, Y. / Su, X. / Yan, X. / Wang, Y. / Liu, W. / Cheng, H. / Wang, Y. / Yang, Q.
History
DepositionNov 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Chitin deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8393
Polymers31,6361
Non-polymers2032
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-26 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.786, 65.420, 106.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chitin deacetylase / / Polysaccharide deacetylase


Mass: 31636.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puccinia striiformis f. sp. tritici (stripe rust fungus)
Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2S4WL56, chitin deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BHO / BENZHYDROXAMIC ACID


Mass: 137.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.1M Sodium malonate, 0.1M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 36799 / % possible obs: 99.2 % / Redundancy: 13 % / Biso Wilson estimate: 16.46 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 4.8
Reflection shellResolution: 1.61→1.64 Å / Rmerge(I) obs: 0.421 / Num. unique obs: 1731

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iw0

2iw0


Resolution: 1.61→26.51 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.5778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 1997 5.49 %
Rwork0.1646 34403 -
obs0.1658 36400 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.94 Å2
Refinement stepCycle: LAST / Resolution: 1.61→26.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 11 298 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691855
X-RAY DIFFRACTIONf_angle_d0.94082530
X-RAY DIFFRACTIONf_chiral_restr0.0598271
X-RAY DIFFRACTIONf_plane_restr0.0053332
X-RAY DIFFRACTIONf_dihedral_angle_d14.9685662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.23131330.18082299X-RAY DIFFRACTION94.45
1.65-1.690.16881390.16622392X-RAY DIFFRACTION98.21
1.69-1.740.19811410.15782424X-RAY DIFFRACTION98.5
1.74-1.80.21791410.15222431X-RAY DIFFRACTION100
1.8-1.860.15731420.15282448X-RAY DIFFRACTION100
1.86-1.940.16821410.15812429X-RAY DIFFRACTION99.81
1.94-2.030.18891420.15772452X-RAY DIFFRACTION99.46
2.03-2.130.17191440.15682470X-RAY DIFFRACTION99.96
2.13-2.270.17491430.15092461X-RAY DIFFRACTION99.96
2.27-2.440.1951430.15782477X-RAY DIFFRACTION100
2.44-2.690.18331440.16132492X-RAY DIFFRACTION99.96
2.69-3.080.17651460.17182496X-RAY DIFFRACTION99.17
3.08-3.870.19951460.16192520X-RAY DIFFRACTION99.81
3.87-26.510.18991520.18032612X-RAY DIFFRACTION97.88

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