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- PDB-8xly: Crystal structure of AtHPPD-Phe complex -

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Basic information

Entry
Database: PDB / ID: 8xly
TitleCrystal structure of AtHPPD-Phe complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex
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
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
: / PHENYLALANINE / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.106 Å
AuthorsDong, J. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: ACS Agric Sci Technol / Year: 2025
Title: Deciphering the Role of the 4-Hydroxyl Group in 4-Hydroxyphenylpyruvate Dioxygenase Catalysis through Structural Analysis
Authors: Ying, R.N. / Zhang, X.J. / Dong, J. / Kandegama, W. / Lin, H.Y. / Dong, J. / Yang, G.F.
#1: Journal: To Be Published
Title: Crystal structure of AtHPPD-Phe complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionDec 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation / citation_author

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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)92,1895
Polymers91,9052
Non-polymers2833
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-38 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.089, 57.131, 62.971
Angle α, β, γ (deg.)97.25, 97.24, 94.80
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 45952.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD, PDS1, At1g06570, F12K11.9 / Production host: Escherichia coli (E. coli)
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-CO / COBALT (II) ION


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


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.39 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.1M Tris/Bicine pH 8.5, 15% (v/v) MPD, 15% (w/v) PEG 1000, 15% (w/v) PEG 3350, 0.03M NaBr, 0.03M NaF, 0.03M NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.106→44.878 Å / Num. obs: 43732 / % possible obs: 97.05 % / Redundancy: 1.77 % / CC1/2: 0.986 / Net I/σ(I): 6.16
Reflection shellResolution: 2.11→2.23 Å / Num. unique obs: 13352 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.106→44.878 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 32.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 2184 4.99 %
Rwork0.2053 --
obs0.2074 43732 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.106→44.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 0 14 232 6003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075931
X-RAY DIFFRACTIONf_angle_d0.8288034
X-RAY DIFFRACTIONf_dihedral_angle_d183517
X-RAY DIFFRACTIONf_chiral_restr0.052885
X-RAY DIFFRACTIONf_plane_restr0.0051053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.106-2.15160.40961260.33722416X-RAY DIFFRACTION92
2.1516-2.20170.32651390.29212646X-RAY DIFFRACTION97
2.2017-2.25670.321340.28932535X-RAY DIFFRACTION97
2.2567-2.31780.34041350.25422591X-RAY DIFFRACTION97
2.3178-2.38590.2761380.23632621X-RAY DIFFRACTION97
2.3859-2.4630.2941380.2442597X-RAY DIFFRACTION97
2.463-2.5510.30421360.24282585X-RAY DIFFRACTION97
2.551-2.65310.35491380.23362635X-RAY DIFFRACTION97
2.6531-2.77380.27831340.21942575X-RAY DIFFRACTION98
2.7738-2.920.26181410.20962673X-RAY DIFFRACTION98
2.92-3.1030.23541380.20532613X-RAY DIFFRACTION98
3.103-3.34250.23591390.19072653X-RAY DIFFRACTION98
3.3425-3.67870.21091350.17982559X-RAY DIFFRACTION97
3.6787-4.21070.20281390.17072630X-RAY DIFFRACTION98
4.2107-5.30370.19391380.16312621X-RAY DIFFRACTION97
5.3037-80.22031360.19972598X-RAY DIFFRACTION98

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