PDB-9kp0: Crystal structure of Oryza sativa HPPD

ID or keywords:

Entry

Database: PDB / ID: 9kp0

Title

Crystal structure of Oryza sativa HPPD

Components

4-hydroxyphenylpyruvate dioxygenase

Keywords

OXIDOREDUCTASE

Function / homology

ACETIC ACID / :

Function and homology information

Biological species

Oryza sativa (Asian cultivated rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Nishio, T. / Nishijima, N. / Kubota, T. / Furuhata, Y. / Kato, Y.

Funding support

1items

Citation

Journal: 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

Deposition	Nov 22, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jul 2, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kp0.cif.gz	178.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9kp0.ent.gz	133.8 KB	Display	PDB format
PDBx/mmJSON format	9kp0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kp0_validation.pdf.gz	453.1 KB	Display	wwPDB validaton report
Full document	9kp0_full_validation.pdf.gz	461.1 KB	Display
Data in XML	9kp0_validation.xml.gz	39.6 KB	Display
Data in CIF	9kp0_validation.cif.gz	54.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kp/9kp0 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/9kp0	HTTPS FTP

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Related structure data

Related structure data	9koyC 9kozC 1sp9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: 4-hydroxyphenylpyruvate dioxygenase

B: 4-hydroxyphenylpyruvate dioxygenase

hetero molecules

94.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	1
Space group name H-M	P1

#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 interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.8 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.02 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 19, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.02 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 65758 / % possible obs: 97.9 % / Redundancy: 3.69 % / CC_1/2: 0.978 / R_merge(I) obs: 0.168 / Net I/σ(I): 6.92
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 3.32 % / R_merge(I) obs: 0.842 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 10263 / CC_1/2: 0.622 / % possible all: 95.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SP9

1sp9

Resolution: 2→45.94 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2265	3288	5 %
R_work	0.1936	62470	-
all	0.195	-	-
obs	-	65758	98.328 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.281 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0 Å²	-0.003 Å²	-0.002 Å²
2-	-	-0.002 Å²	0.002 Å²
3-	-	-	0.002 Å²

Refinement step

Cycle: LAST / Resolution: 2→45.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5995	0	18	497	6510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	6140
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5672
X-RAY DIFFRACTION	r_angle_refined_deg	1.315	1.808	8324
X-RAY DIFFRACTION	r_angle_other_deg	0.464	1.735	12994
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.782	5	789
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.726	5	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.724	10	886
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.676	10	296
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	891
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7543
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1525
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	1182
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	5230
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	2967
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3172
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	476
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.072	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.109	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.235	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.242	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.348	0.2	22
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.138	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.099	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.843	2.869	3175
X-RAY DIFFRACTION	r_mcbond_other	1.839	2.869	3175
X-RAY DIFFRACTION	r_mcangle_it	3.008	5.141	3957
X-RAY DIFFRACTION	r_mcangle_other	3.008	5.142	3958
X-RAY DIFFRACTION	r_scbond_it	2.279	3.18	2965
X-RAY DIFFRACTION	r_scbond_other	2.279	3.182	2966
X-RAY DIFFRACTION	r_scangle_it	3.776	5.703	4367
X-RAY DIFFRACTION	r_scangle_other	3.775	5.704	4368
X-RAY DIFFRACTION	r_lrange_it	5.744	32.065	6799
X-RAY DIFFRACTION	r_lrange_other	5.656	30.989	6681

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2-2.052	0.292	237	0.267	4514	0.268	4965	0.947	0.953	95.6898	0.267
2.052-2.108	0.343	230	0.353	4373	0.352	4797	0.885	0.887	95.9558	0.334
2.108-2.169	0.26	226	0.211	4296	0.213	4662	0.956	0.97	96.997	0.204
2.169-2.236	0.263	223	0.25	4232	0.251	4563	0.955	0.964	97.6331	0.244
2.236-2.309	0.372	217	0.34	4110	0.341	4437	0.817	0.87	97.5208	0.317
2.309-2.389	0.219	210	0.18	3992	0.182	4256	0.968	0.98	98.7312	0.171
2.389-2.479	0.232	203	0.18	3872	0.183	4123	0.967	0.98	98.8358	0.171
2.479-2.58	0.233	196	0.176	3722	0.179	3959	0.963	0.981	98.9644	0.167
2.58-2.695	0.218	188	0.175	3558	0.177	3783	0.971	0.979	99.0219	0.164
2.695-2.826	0.213	181	0.165	3442	0.168	3656	0.97	0.983	99.0974	0.16
2.826-2.978	0.229	168	0.177	3206	0.18	3401	0.965	0.981	99.2061	0.175
2.978-3.158	0.208	163	0.177	3096	0.179	3282	0.972	0.981	99.2992	0.176
3.158-3.375	0.205	153	0.181	2899	0.182	3072	0.974	0.982	99.349	0.181
3.375-3.643	0.235	142	0.188	2703	0.191	2868	0.968	0.981	99.1981	0.19
3.643-3.989	0.215	130	0.194	2475	0.195	2628	0.976	0.975	99.1248	0.2
3.989-4.455	0.167	119	0.136	2245	0.138	2372	0.985	0.989	99.6627	0.152
4.455-5.136	0.178	105	0.135	2002	0.137	2109	0.985	0.99	99.9052	0.157
5.136-6.271	0.181	89	0.18	1687	0.18	1779	0.98	0.985	99.8314	0.204
6.271-8.787	0.222	69	0.195	1305	0.196	1378	0.978	0.98	99.7097	0.224
8.787-45.94	0.217	39	0.216	742	0.216	782	0.967	0.975	99.8721	0.268

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