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- PDB-9kp0: Crystal structure of Oryza sativa HPPD -

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Basic information

Entry
Database: PDB / ID: 9kp0
TitleCrystal structure of Oryza sativa HPPD
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE
Function / homologyACETIC ACID / :
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82117
Polymers93,8582
Non-polymers96315
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-341 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.110, 64.590, 73.160
Angle α, β, γ (deg.)101.387, 107.961, 97.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase


Mass: 46929.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate (pH 4.5), 20 vol% PEG1000, and 0.2 M zinc acetate 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: 1.02 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65758 / % possible obs: 97.9 % / Redundancy: 3.69 % / CC1/2: 0.978 / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.92
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 10263 / CC1/2: 0.622 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SP9

1sp9


Resolution: 2→45.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.61 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2265 3288 5 %
Rwork0.1936 62470 -
all0.195 --
obs-65758 98.328 %
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: 28.281 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.003 Å2-0.002 Å2
2---0.002 Å20.002 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 2→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 18 497 6510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126140
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165672
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.8088324
X-RAY DIFFRACTIONr_angle_other_deg0.4641.73512994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.726554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72410886
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.67610296
X-RAY DIFFRACTIONr_chiral_restr0.0620.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021525
X-RAY DIFFRACTIONr_nbd_refined0.20.21182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.25230
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22967
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23172
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2476
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.225
X-RAY DIFFRACTIONr_nbd_other0.2420.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3480.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1380.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0990.23
X-RAY DIFFRACTIONr_mcbond_it1.8432.8693175
X-RAY DIFFRACTIONr_mcbond_other1.8392.8693175
X-RAY DIFFRACTIONr_mcangle_it3.0085.1413957
X-RAY DIFFRACTIONr_mcangle_other3.0085.1423958
X-RAY DIFFRACTIONr_scbond_it2.2793.182965
X-RAY DIFFRACTIONr_scbond_other2.2793.1822966
X-RAY DIFFRACTIONr_scangle_it3.7765.7034367
X-RAY DIFFRACTIONr_scangle_other3.7755.7044368
X-RAY DIFFRACTIONr_lrange_it5.74432.0656799
X-RAY DIFFRACTIONr_lrange_other5.65630.9896681
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
2-2.0520.2922370.26745140.26849650.9470.95395.68980.267
2.052-2.1080.3432300.35343730.35247970.8850.88795.95580.334
2.108-2.1690.262260.21142960.21346620.9560.9796.9970.204
2.169-2.2360.2632230.2542320.25145630.9550.96497.63310.244
2.236-2.3090.3722170.3441100.34144370.8170.8797.52080.317
2.309-2.3890.2192100.1839920.18242560.9680.9898.73120.171
2.389-2.4790.2322030.1838720.18341230.9670.9898.83580.171
2.479-2.580.2331960.17637220.17939590.9630.98198.96440.167
2.58-2.6950.2181880.17535580.17737830.9710.97999.02190.164
2.695-2.8260.2131810.16534420.16836560.970.98399.09740.16
2.826-2.9780.2291680.17732060.1834010.9650.98199.20610.175
2.978-3.1580.2081630.17730960.17932820.9720.98199.29920.176
3.158-3.3750.2051530.18128990.18230720.9740.98299.3490.181
3.375-3.6430.2351420.18827030.19128680.9680.98199.19810.19
3.643-3.9890.2151300.19424750.19526280.9760.97599.12480.2
3.989-4.4550.1671190.13622450.13823720.9850.98999.66270.152
4.455-5.1360.1781050.13520020.13721090.9850.9999.90520.157
5.136-6.2710.181890.1816870.1817790.980.98599.83140.204
6.271-8.7870.222690.19513050.19613780.9780.9899.70970.224
8.787-45.940.217390.2167420.2167820.9670.97599.87210.268

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