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- PDB-8hf9: The structure of chitin deacetylase Pst_13661 from Puccinia strii... -

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Basic information

Entry
Database: PDB / ID: 8hf9
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
NodB homology domain-containing protein
Similarity search - Component
Biological speciesPuccinia striiformis f. sp. tritici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 10, 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 9, 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)31,7022
Polymers31,6361
Non-polymers651
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.669, 65.727, 105.362
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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1260mM Ammonium sulfate, 100mM Sodium cacodylate/Hydrochloric acid pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 20522 / % possible obs: 99.3 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.45 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 4.8
Reflection shellResolution: 1.96→1.99 Å / Rmerge(I) obs: 0.413 / Num. unique obs: 915

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iw0

2iw0


Resolution: 1.96→33.96 Å / SU ML: 0.2218 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.0208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1969 9.89 %
Rwork0.1947 17934 -
obs0.1977 19903 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.44 Å2
Refinement stepCycle: LAST / Resolution: 1.96→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 1 167 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011845
X-RAY DIFFRACTIONf_angle_d0.95832518
X-RAY DIFFRACTIONf_chiral_restr0.0592271
X-RAY DIFFRACTIONf_plane_restr0.0056330
X-RAY DIFFRACTIONf_dihedral_angle_d18.1223661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.30271230.23641109X-RAY DIFFRACTION85.26
2.01-2.060.26861390.22811226X-RAY DIFFRACTION94.66
2.06-2.120.2471360.21681244X-RAY DIFFRACTION96.5
2.12-2.190.25031410.2071285X-RAY DIFFRACTION97.74
2.19-2.270.27961310.25331185X-RAY DIFFRACTION93.2
2.27-2.360.30891350.1971239X-RAY DIFFRACTION95.62
2.36-2.470.24651420.19961284X-RAY DIFFRACTION98.82
2.47-2.60.24251440.19821299X-RAY DIFFRACTION99.31
2.6-2.760.23131410.2021303X-RAY DIFFRACTION99.38
2.76-2.980.251440.22021312X-RAY DIFFRACTION99.59
2.98-3.270.24751450.20051323X-RAY DIFFRACTION99.93
3.27-3.750.21221440.18231327X-RAY DIFFRACTION99.59
3.75-4.720.13971480.15271357X-RAY DIFFRACTION100
4.72-33.960.22411560.19391441X-RAY DIFFRACTION99.94

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