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- PDB-9js2: Complex structure of AtHPPD with inhibitor YH23570 -

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Basic information

Entry
Database: PDB / ID: 9js2
TitleComplex structure of AtHPPD with inhibitor YH23570
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / Complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / identical protein binding / cytoplasm
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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsYing, R.-N. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Complex structure of AtHPPD with inhibitor YH23570
Authors: Ying, R.-N. / Lin, H.-Y. / Yang, G.-F.
History
DepositionSep 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7713
Polymers44,3421
Non-polymers4292
Water2,774154
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5426
Polymers88,6842
Non-polymers8594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area3270 Å2
ΔGint-10 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.153, 83.737, 65.740
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44341.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD, PDS1, At1g06570, F12K11.9 / Production host: Escherichia coli (E. coli)
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-A1L4S / 1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-propoxy-quinoxalin-2-one


Mass: 370.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl pH 8.5, 0.1M Bicine pH 8.5, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 25%(w/v) MPD, 25%(w/v) PEG 1000, 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.94→64.72 Å / Num. obs: 28952 / % possible obs: 94.3 % / Redundancy: 3.9 % / CC1/2: 0.975 / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.6
Reflection shellResolution: 1.94→2.04 Å / Num. unique obs: 1015 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→64.72 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 1419 4.95 %
Rwork0.1915 --
obs0.1932 28665 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→64.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 28 154 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072959
X-RAY DIFFRACTIONf_angle_d0.8384013
X-RAY DIFFRACTIONf_dihedral_angle_d8.0442372
X-RAY DIFFRACTIONf_chiral_restr0.052438
X-RAY DIFFRACTIONf_plane_restr0.006522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.00520.33261270.2652365X-RAY DIFFRACTION81
2.0052-2.08550.33321340.24832503X-RAY DIFFRACTION86
2.0855-2.18040.29471400.23542888X-RAY DIFFRACTION99
2.1804-2.29540.27121290.21872590X-RAY DIFFRACTION89
2.2954-2.43920.2561420.19882934X-RAY DIFFRACTION100
2.4392-2.62750.23191340.20252937X-RAY DIFFRACTION100
2.6275-2.89190.24171560.19732638X-RAY DIFFRACTION92
2.8919-3.31040.22181570.17832922X-RAY DIFFRACTION100
3.3104-4.17070.19081470.1612495X-RAY DIFFRACTION86
4.1707-100.18111530.17432974X-RAY DIFFRACTION99

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