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- PDB-8hfa: The structure of chitin deacetylase VdPDA1 from Verticillium dahliae -

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Basic information

Entry
Database: PDB / ID: 8hfa
TitleThe structure of chitin deacetylase VdPDA1 from Verticillium dahliae
ComponentsNodB homology domain-containing protein
KeywordsHYDROLASE / Chitin deacetylase / Plant pathogenic fungi / Virulence factor
Function / homologyNodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / NodB homology domain-containing protein
Function and homology information
Biological speciesVerticillium dahliae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsLiu, L. / 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 23, 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: NodB homology domain-containing protein
B: NodB homology domain-containing protein
C: NodB homology domain-containing protein
D: NodB homology domain-containing protein
E: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,39310
Polymers144,0665
Non-polymers3275
Water11,656647
1
A: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8792
Polymers28,8131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-37 kcal/mol
Surface area9100 Å2
MethodPISA
2
B: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8792
Polymers28,8131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area9080 Å2
MethodPISA
3
C: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8792
Polymers28,8131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area9030 Å2
MethodPISA
4
D: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8792
Polymers28,8131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-37 kcal/mol
Surface area9140 Å2
MethodPISA
5
E: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8792
Polymers28,8131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.617, 125.899, 127.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
NodB homology domain-containing protein / chitin deacetylase / polysaccharide deacetylase


Mass: 28813.236 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verticillium dahliae (fungus) / Gene: VD0003_g2480 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2J8E0S3, chitin deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 3.85 Å3/Da / Density % sol: 68.02 %
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: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 65718 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 25.92 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 4.1
Reflection shellResolution: 2.64→2.7 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 3227

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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: 2.64→37.36 Å / SU ML: 0.2377 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227 1996 3.05 %
Rwork0.1924 63548 -
obs0.1934 65544 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 2.64→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 5 647 9197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00788775
X-RAY DIFFRACTIONf_angle_d0.988111925
X-RAY DIFFRACTIONf_chiral_restr0.05551300
X-RAY DIFFRACTIONf_plane_restr0.00721525
X-RAY DIFFRACTIONf_dihedral_angle_d14.1073220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.70.28051280.23313969X-RAY DIFFRACTION87.86
2.7-2.770.28641430.21964517X-RAY DIFFRACTION100
2.77-2.860.23831410.2034529X-RAY DIFFRACTION100
2.86-2.950.25231440.20724538X-RAY DIFFRACTION100
2.95-3.050.24871390.21054526X-RAY DIFFRACTION99.98
3.05-3.180.24451440.22644553X-RAY DIFFRACTION100
3.18-3.320.23351390.19414562X-RAY DIFFRACTION100
3.32-3.50.22141480.19054543X-RAY DIFFRACTION100
3.5-3.710.20051390.18464578X-RAY DIFFRACTION100
3.71-40.22321470.17754571X-RAY DIFFRACTION100
4-4.40.20151450.16474594X-RAY DIFFRACTION100
4.4-5.040.20641450.16244622X-RAY DIFFRACTION100
5.04-6.340.21391470.19384680X-RAY DIFFRACTION99.98
6.34-37.360.22991470.20684766X-RAY DIFFRACTION98.26

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