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- PDB-8he2: The structure of chitin deacetylase Pst_13661 from Puccinia strii... -

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Basic information

Entry
Database: PDB / ID: 8he2
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 / 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
Chem-LMI / NodB homology domain-containing protein
Similarity search - Component
Biological speciesPuccinia striiformis f. sp. tritici (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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)32,0393
Polymers31,6361
Non-polymers4032
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.859, 65.528, 105.966
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 (fungus)
Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2S4WL56, chitin deacetylase
#2: Chemical ChemComp-LMI / tert-butyl N-[3-[[4-(oxidanylcarbamoyl)phenyl]methylamino]-3-oxidanylidene-propyl]carbamate


Mass: 337.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.76 %
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: 36811 / % possible obs: 97.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 13.02 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.5
Reflection shellResolution: 1.61→1.64 Å / Rmerge(I) obs: 0.442 / Num. unique obs: 1643

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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→20.91 Å / SU ML: 0.1328 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.8493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.18 1963 5.63 %
Rwork0.1573 32921 -
obs0.1586 34884 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.98 Å2
Refinement stepCycle: LAST / Resolution: 1.61→20.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 25 360 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651884
X-RAY DIFFRACTIONf_angle_d1.00352574
X-RAY DIFFRACTIONf_chiral_restr0.057274
X-RAY DIFFRACTIONf_plane_restr0.0056338
X-RAY DIFFRACTIONf_dihedral_angle_d14.3443685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.25361280.18082172X-RAY DIFFRACTION89.77
1.65-1.70.22811350.17112284X-RAY DIFFRACTION93.25
1.7-1.750.18591390.16422313X-RAY DIFFRACTION94.09
1.75-1.80.21351320.15922257X-RAY DIFFRACTION93.21
1.8-1.870.17141350.15222282X-RAY DIFFRACTION93.21
1.87-1.940.17291390.15452277X-RAY DIFFRACTION93.83
1.94-2.030.17521380.15062339X-RAY DIFFRACTION94.98
2.03-2.140.17381450.15312379X-RAY DIFFRACTION96.52
2.14-2.270.171430.14952378X-RAY DIFFRACTION96.92
2.27-2.440.17811410.15152409X-RAY DIFFRACTION97.29
2.44-2.690.18011450.16032415X-RAY DIFFRACTION97.01
2.69-3.080.20591440.16422423X-RAY DIFFRACTION96.58
3.08-3.870.14791480.14962489X-RAY DIFFRACTION98.29
3.87-20.910.18151510.16262504X-RAY DIFFRACTION94.22

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