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- PDB-9lia: Crystal structure of AaHPPD-ZD001 complex -

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Basic information

Entry
Database: PDB / ID: 9lia
TitleCrystal structure of AaHPPD-ZD001 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / Inhibitor
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / Golgi membrane / endoplasmic reticulum membrane / protein homodimerization activity / 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
: / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.495 Å
AuthorsYang, G.-F. / Lin, H.-Y. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Repurposing 4-Hydroxyphenylpyruvate dioxygenase inhibitors as novel agents for mosquito control: A structure-based design approach.
Authors: Dong, J. / Fu, Y.X. / Zheng, B.F. / Chen, M.X. / Chen, Q. / Wishwajith, K. / Dong, J. / Lin, H.Y. / Yang, G.F.
History
DepositionJan 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7023
Polymers43,2821
Non-polymers4202
Water7,008389
1
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4046
Polymers86,5642
Non-polymers8414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4040 Å2
ΔGint-13 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.984, 83.841, 59.184
Angle α, β, γ (deg.)90.00, 101.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-619-

HOH

21B-703-

HOH

31B-856-

HOH

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase


Mass: 43281.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL014600 / Production host: Escherichia coli 0.1288 (bacteria) / References: UniProt: Q16FX9
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-A1L7D / 5-(1-methyl-5-oxidanyl-pyrazol-4-yl)carbonyl-2-(phenylmethyl)isoindole-1,3-dione


Mass: 361.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1M sodium citrate (pH 5.0), 10% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.459→28.96 Å / Num. obs: 58485 / % possible obs: 98.5 % / Redundancy: 5 % / CC1/2: 0.987 / Net I/σ(I): 2
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 5563 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.495→28.96 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 17.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 2924 5 %
Rwork0.1658 --
obs0.1668 58485 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.495→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 28 389 3422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063048
X-RAY DIFFRACTIONf_angle_d0.8544134
X-RAY DIFFRACTIONf_dihedral_angle_d12.9691090
X-RAY DIFFRACTIONf_chiral_restr0.082445
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.495-1.51910.22041260.19182404X-RAY DIFFRACTION90
1.5191-1.54530.21771380.18962606X-RAY DIFFRACTION98
1.5453-1.57340.20471370.1782616X-RAY DIFFRACTION98
1.5734-1.60370.2021380.17262619X-RAY DIFFRACTION97
1.6037-1.63640.18431390.16882629X-RAY DIFFRACTION98
1.6364-1.6720.16791390.1672646X-RAY DIFFRACTION98
1.672-1.71090.20141380.16932628X-RAY DIFFRACTION98
1.7109-1.75370.20461390.18032632X-RAY DIFFRACTION98
1.7537-1.80110.21651390.18042645X-RAY DIFFRACTION99
1.8011-1.8540.18531400.17462657X-RAY DIFFRACTION99
1.854-1.91390.21011390.17382654X-RAY DIFFRACTION99
1.9139-1.98230.19891400.16492643X-RAY DIFFRACTION99
1.9823-2.06160.1761400.16612662X-RAY DIFFRACTION99
2.0616-2.15540.17311400.16472670X-RAY DIFFRACTION100
2.1554-2.2690.17971420.16632698X-RAY DIFFRACTION99
2.269-2.41110.17961400.16682650X-RAY DIFFRACTION99
2.4111-2.59720.18281410.17732688X-RAY DIFFRACTION100
2.5972-2.85830.20371410.17842681X-RAY DIFFRACTION100
2.8583-3.27140.18131410.16652679X-RAY DIFFRACTION100
3.2714-4.11980.17551430.15022709X-RAY DIFFRACTION100
4.1198-80.16451440.14912745X-RAY DIFFRACTION100

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