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- PDB-21wf: Structure of Rice HPPD in complex with MST -

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Basic information

Entry
Database: PDB / ID: 21wf
TitleStructure of Rice HPPD in complex with MST
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / metal ion 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
Chem-92L / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsChen, Y.H. / Zhang, C.R. / Wang, M.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Rice HPPD in complex with MST
Authors: Chen, Y.H. / Zhang, C.R. / Wang, M.H.
History
DepositionDec 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: 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)94,7696
Polymers93,9782
Non-polymers7904
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-33 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.830, 157.830, 83.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase


Mass: 46989.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OSJNBa0085K21.52, P0669G09.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6H4V1
#2: Chemical ChemComp-92L / 2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione / Mesotrione


Mass: 339.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H13NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M Mgcl2.6H2O, 0.1M BIS-TRIS PH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.32→28.62 Å / Num. obs: 45794 / % possible obs: 99.67 % / Redundancy: 6 % / CC1/2: 1 / Rmerge(I) obs: 0.009493 / Rpim(I) all: 0.009493 / Rrim(I) all: 0.01343 / Net I/σ(I): 36.16
Reflection shellResolution: 2.32→2.403 Å / Rmerge(I) obs: 0.2879 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 8836 / CC1/2: 0.775 / Rpim(I) all: 0.2879 / Rrim(I) all: 0.4071

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
xia2data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→28.62 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 2349 5.13 %
Rwork0.2259 --
obs0.2283 45787 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 48 40 5910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076009
X-RAY DIFFRACTIONf_angle_d0.9358158
X-RAY DIFFRACTIONf_dihedral_angle_d15.3212120
X-RAY DIFFRACTIONf_chiral_restr0.051862
X-RAY DIFFRACTIONf_plane_restr0.0081110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.40041300.3282454X-RAY DIFFRACTION98
2.37-2.420.36641420.31252483X-RAY DIFFRACTION99
2.42-2.470.35051270.29962522X-RAY DIFFRACTION99
2.48-2.540.39031530.30042510X-RAY DIFFRACTION100
2.54-2.610.41471070.31572544X-RAY DIFFRACTION100
2.61-2.680.38781330.31462542X-RAY DIFFRACTION100
2.68-2.770.34971300.30182569X-RAY DIFFRACTION100
2.77-2.870.34261660.28322494X-RAY DIFFRACTION100
2.87-2.980.33541520.28772519X-RAY DIFFRACTION100
2.98-3.120.3581250.28872529X-RAY DIFFRACTION100
3.12-3.280.34511430.28312560X-RAY DIFFRACTION100
3.28-3.490.29141420.24612573X-RAY DIFFRACTION100
3.49-3.760.25131450.23442549X-RAY DIFFRACTION100
3.76-4.130.26691510.21812565X-RAY DIFFRACTION100
4.13-4.730.22791280.18232607X-RAY DIFFRACTION100
4.73-5.950.2081300.19262657X-RAY DIFFRACTION100
5.95-28.620.23731450.18672761X-RAY DIFFRACTION100

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