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- PDB-9koz: Crystal structure of Arabidopsis thaliana HPPD complexed with ipt... -

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Basic information

Entry
Database: PDB / ID: 9koz
TitleCrystal structure of Arabidopsis thaliana HPPD complexed with iptriazopyrid
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / 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: 2.15 Å
AuthorsNishio, T. / Nishijima, N. / Kubota, T. / Furuhata, Y. / Kato, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Mechanism of Herbicidal Action and Rice Selectivity of Iptriazopyrid: A Novel Azole Carboxamide-Based Inhibitor of 4-Hydroxyphenylpyruvate Dioxygenase.
Authors: Nishio, T. / Nishijima, N. / Kubota, T. / Furuhata, Y. / Nanao, Y. / Permana, H. / Furuhashi, T. / Kato, Y.
History
DepositionNov 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,93612
Polymers194,9714
Non-polymers1,9658
Water6,990388
1
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4686
Polymers97,4852
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area32520 Å2
MethodPISA
2
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4686
Polymers97,4852
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-18 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.160, 96.040, 97.820
Angle α, β, γ (deg.)90.000, 92.806, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48742.633 Da / Num. of mol.: 4
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 BL21(DE3) (bacteria)
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-A1L59 / iptriazopyrid / ~{N}-(5-methyl-1,3,4-oxadiazol-2-yl)-3-(propan-2-ylsulfonylmethyl)-5-(trifluoromethyl)-[1,2,4]triazolo[4,3-a]pyridine-8-carboxamide


Mass: 432.378 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H15F3N6O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.0), 32 or 28 vol% polyethylene glycol (PEG) 400, and 15 or 10 vol% 2-propanol 2 mM iptriazopyrid and 2 mM CoCl2

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.025 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.025 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 96459 / % possible obs: 99.7 % / Redundancy: 6.69 % / CC1/2: 0.991 / Rmerge(I) obs: 0.239 / Net I/σ(I): 6.14
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 5.63 % / Rmerge(I) obs: 2.988 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 15372 / CC1/2: 0.421 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SP9

1sp9


Resolution: 2.15→48.022 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.758 / SU ML: 0.229 / Cross valid method: FREE R-VALUE / ESU R: 0.268 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2662 4744 4.999 %
Rwork0.211 90160 -
all0.214 --
obs-94904 98.139 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.468 Å2
Baniso -1Baniso -2Baniso -3
1-0.022 Å20 Å20.001 Å2
2---0.006 Å2-0 Å2
3----0.016 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12352 0 120 388 12860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212755
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611846
X-RAY DIFFRACTIONr_angle_refined_deg1.241.83417225
X-RAY DIFFRACTIONr_angle_other_deg0.4381.75427353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72251569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.0776.8100
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg12.61212.58
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.182102128
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.02410581
X-RAY DIFFRACTIONr_chiral_restr0.0570.21843
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022976
X-RAY DIFFRACTIONr_nbd_refined0.2030.22360
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.210915
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26119
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.26612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2542
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.231
X-RAY DIFFRACTIONr_nbd_other0.2310.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.210
X-RAY DIFFRACTIONr_mcbond_it3.1794.9326324
X-RAY DIFFRACTIONr_mcbond_other3.1794.9326324
X-RAY DIFFRACTIONr_mcangle_it4.9378.8427877
X-RAY DIFFRACTIONr_mcangle_other4.9368.8437878
X-RAY DIFFRACTIONr_scbond_it3.6815.3286431
X-RAY DIFFRACTIONr_scbond_other3.6815.3286432
X-RAY DIFFRACTIONr_scangle_it5.7239.6249348
X-RAY DIFFRACTIONr_scangle_other5.7239.6249349
X-RAY DIFFRACTIONr_lrange_it8.33448.91213786
X-RAY DIFFRACTIONr_lrange_other8.32948.88313734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.15-2.2060.4593560.42667670.42871250.8220.84699.97190.403
2.206-2.2660.5662600.54249760.54369560.7820.79275.27310.641
2.266-2.3320.3993360.37363710.37567080.8760.88399.98510.352
2.332-2.4030.3623280.31862290.3265570.8980.9171000.294
2.403-2.4820.3163150.28959940.29163100.9270.93699.98420.267
2.482-2.5690.3223080.26858490.2761570.9250.9481000.246
2.569-2.6650.2872980.23556730.23759710.9420.9621000.211
2.665-2.7740.2932830.22253630.22656460.9440.9671000.2
2.774-2.8970.2772760.20852510.21255270.950.9731000.186
2.897-3.0380.2752620.20349750.20752370.9510.9741000.181
3.038-3.2010.2552500.19347540.19650040.9580.9771000.177
3.201-3.3940.2432350.18844640.19147000.9650.9899.97870.182
3.394-3.6270.232220.17642170.17944450.9650.98299.8650.172
3.627-3.9160.2212070.17639400.17941610.9690.98299.66350.176
3.916-4.2870.2181900.15536120.15838070.9720.98699.86870.165
4.287-4.7880.1981730.14532770.14734670.9770.98899.50970.16
4.788-5.520.2651530.17329030.17830630.9590.98399.77150.194
5.52-6.7380.271300.2124790.21326140.9620.97899.80870.234
6.738-9.4370.2131020.1719290.17320370.9760.98399.70550.206
9.437-48.0220.238600.19711380.19912040.960.97799.50170.244

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