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- PDB-8jbw: Crystal structure of ZtHPPD-(+)-Usnic acid complex -

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Basic information

Entry
Database: PDB / ID: 8jbw
TitleCrystal structure of ZtHPPD-(+)-Usnic acid complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / inhibitor
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / metal ion binding
Similarity search - Function
4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
Chem-AIY / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesZymoseptoria tritici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLin, H.-Y. / Dong, J. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Discovery and Development of 4-Hydroxyphenylpyruvate Dioxygenase as a Novel Crop Fungicide Target.
Authors: Yu, X.H. / Dong, J. / Fan, C.P. / Chen, M.X. / Li, M. / Zheng, B.F. / Hu, Y.F. / Lin, H.Y. / Yang, G.F.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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:
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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1953
Polymers46,7911
Non-polymers4032
Water00
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3896
Polymers93,5832
Non-polymers8064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3090 Å2
ΔGint-6 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.348, 110.348, 80.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase / 4HPPD / HPD / HPPDase


Mass: 46791.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymoseptoria tritici (fungus) / Gene: HPPD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O42764, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AIY / (9bR)-2,6-diethanoyl-8,9b-dimethyl-3,7,9-tris(oxidanyl)dibenzofuran-1-one / (+)-Usnic acid / (+)-Usniacin


Mass: 344.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16O7
Has ligand of interestN
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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.15M (NH4)2SO4, 0.1M MES pH6.0, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 14995 / % possible obs: 99.9 % / Redundancy: 25 % / CC1/2: 1 / Rmerge(I) obs: 0.117 / Net I/σ(I): 26.4
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 735 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→49.35 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3025 741 5.07 %
Rwork0.2526 --
obs0.2552 14605 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 26 0 2867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082940
X-RAY DIFFRACTIONf_angle_d1.0964004
X-RAY DIFFRACTIONf_dihedral_angle_d24.5181022
X-RAY DIFFRACTIONf_chiral_restr0.058435
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.860.45881480.37982703X-RAY DIFFRACTION97
2.86-3.140.32191500.29892740X-RAY DIFFRACTION98
3.14-3.60.3621290.2692777X-RAY DIFFRACTION98
3.6-4.530.28161510.24982662X-RAY DIFFRACTION94
4.53-49.350.2731630.2242982X-RAY DIFFRACTION99

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