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- PDB-9s4a: Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in compl... -

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Basic information

Entry
Database: PDB / ID: 9s4a
TitleArabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Topramezone (Mn)
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / Phenylalanine catabolism / Tyrosine catabolism / Iron / Metal-binding / 4-hydroxyphenylpyruvate / homogentisic acid
Function / homology
Function and homology information


vitamin E biosynthetic process / 4-hydroxyphenylpyruvate dioxygenase / plastoquinone biosynthetic process / 4-hydroxyphenylpyruvate dioxygenase activity / carotenoid biosynthetic process / L-tyrosine catabolic process / L-phenylalanine catabolic process / chloroplast / iron ion binding / mitochondrion ...vitamin E biosynthetic process / 4-hydroxyphenylpyruvate dioxygenase / plastoquinone biosynthetic process / 4-hydroxyphenylpyruvate dioxygenase activity / carotenoid biosynthetic process / L-tyrosine catabolic process / L-phenylalanine catabolic process / chloroplast / iron ion binding / mitochondrion / extracellular region / identical protein binding / cytosol / 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-GJL / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAlshref, F.M. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, Saudi Arabia, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Saudi Ministry of EducationDM8000S4747 Saudi Arabia
CitationJournal: To Be Published
Title: Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Topramezone (Mn)
Authors: Alshref, F.M. / Dhingra, S. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
History
DepositionJul 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7613
Polymers45,3431
Non-polymers4182
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Native mass spectrometry and gel foltration confirms the monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16750 Å2
Unit cell
Length a, b, c (Å)76.915, 84.185, 61.536
Angle α, β, γ (deg.)90.000, 102.037, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

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Components

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


Mass: 45342.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Missing residues were unstructured / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD, PDS1, At1g06570, F12K11.9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GJL / 4-[3-(4,5-dihydro-1,2-oxazol-3-yl)-2-methyl-4-methylsulfonyl-phenyl]carbonyl-2-methyl-1~{H}-pyrazol-3-one


Mass: 363.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: Morpheus F4, 0.1 M Carboxylic acids, 0.1 M Buffer System 1 6.5, 37.5 % v/v Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.94056 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94056 Å / Relative weight: 1
ReflectionResolution: 1.65→60.21 Å / Num. obs: 46116 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.058 / Rrim(I) all: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2302 / CC1/2: 0.715 / Rpim(I) all: 0.639 / Rrim(I) all: 1.202 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→60.18 Å / SU ML: 0.1821 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1994 2345 5.09 %
Rwork0.1652 43719 -
obs0.1669 46064 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→60.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 26 286 3278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663099
X-RAY DIFFRACTIONf_angle_d0.9684196
X-RAY DIFFRACTIONf_chiral_restr0.0876450
X-RAY DIFFRACTIONf_plane_restr0.0081548
X-RAY DIFFRACTIONf_dihedral_angle_d18.3241154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.2611390.25622550X-RAY DIFFRACTION98.53
1.68-1.720.22031400.2282549X-RAY DIFFRACTION99.93
1.72-1.760.21431210.21522579X-RAY DIFFRACTION99.96
1.76-1.80.27511420.1972557X-RAY DIFFRACTION99.82
1.8-1.850.24961170.19592570X-RAY DIFFRACTION99.85
1.85-1.910.20691500.18552571X-RAY DIFFRACTION99.93
1.91-1.970.23041340.18622575X-RAY DIFFRACTION99.89
1.97-2.040.23161190.1672595X-RAY DIFFRACTION99.85
2.04-2.120.18441330.16452534X-RAY DIFFRACTION99.81
2.12-2.220.22311370.15572577X-RAY DIFFRACTION100
2.22-2.330.21600.16252542X-RAY DIFFRACTION100
2.33-2.480.2081370.16262597X-RAY DIFFRACTION99.85
2.48-2.670.20941720.16862529X-RAY DIFFRACTION100
2.67-2.940.1791320.16562574X-RAY DIFFRACTION99.89
2.94-3.370.20691430.15762590X-RAY DIFFRACTION99.89
3.37-4.240.15291240.14122604X-RAY DIFFRACTION99.96
4.24-60.180.19151450.15662626X-RAY DIFFRACTION99.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17503985107-0.3306145425910.2719654226071.92560210539-0.3171453651060.958308174849-0.0380715894931-0.1532469243490.08948215035030.3106053408070.00591541657335-0.320698845834-0.1048340335140.10321080568-0.03595082297170.149854133235-0.0154660469356-0.03079580938470.177022805702-0.0111188302430.17071603423415.6917700419-4.36635221689.73359628344
26.25818445724-1.70692854562-5.132578118930.491681930471.524496914565.08803871898-0.00210957313882-0.3708976506520.1943076666680.2440322649690.0271579246494-0.023476937314-0.0801131700824-0.0851942951861-0.01935767346290.4948054088160.00704027967268-0.02081273868640.344782927156-0.1029968497860.14386827858212.450904938-1.8353050187722.74607031
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - B35 - 5011
22chain BBC601

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