20ZQ | pdb_000020zq

Crystal structure of rice HPPD

PDB DOI: https://doi.org/10.2210/pdb20ZQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oryza sativa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-03 Released: 2026-06-10
Deposition Author(s): Chen, L., Ran, T., Wang, W.W., Zhang, B.L.
Funding Organization(s): Jiangsu Key Research and Development Program, the Basic Research Program of Jiangsu, Zhongshan Biological Breeding Laboratory

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.243 (Depositor), 0.254 (DCC)
R-Value Work:
0.199 (Depositor), 0.214 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

structure of rice hydroxyphenylpyruvate dioxygenase

Chen, L., Ran, T.T., Wang, W.W., Zhang, B.L.

To be published.

Macromolecule Content

Total Structure Weight: 193.39 kDa
Atom Count: 13,261
Modeled Residue Count: 1,643
Deposited Residue Count: 1,816
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A, B, C, D	454	Oryza sativa	Mutation(s): 0
UniProt
Find proteins for A0A0E0G1W2 (Oryza nivara) Explore A0A0E0G1W2 Go to UniProtKB: A0A0E0G1W2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0E0G1W2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth D]	E [auth A], F [auth A], L [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth D]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth D]	G [auth A], M [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	I [auth A], J [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243 (Depositor), 0.254 (DCC)
R-Value Work: 0.199 (Depositor), 0.214 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.064	α = 90
b = 93.436	β = 109.85
c = 113.957	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Jiangsu Key Research and Development Program	China	BE2022365
the Basic Research Program of Jiangsu	China	BK20241182
Zhongshan Biological Breeding Laboratory	China	ZSBBL-KY2023-04