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- PDB-8wk2: Crystal structure of AtHPPD-F419Y+Y13287 complex -

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Basic information

Entry
Database: PDB / ID: 8wk2
TitleCrystal structure of AtHPPD-F419Y+Y13287 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / Complex
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / identical protein 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-92X / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.806 Å
AuthorsYang, G.-F. / Lin, H.-Y. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of AtHPPD-F419Y+Y13287 complex
Authors: Yang, G.-F. / Lin, H.-Y. / Dong, J.
History
DepositionSep 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4463
Polymers45,9691
Non-polymers4772
Water4,432246
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8926
Polymers91,9372
Non-polymers9554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3290 Å2
ΔGint-13 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.908, 83.814, 61.997
Angle α, β, γ (deg.)90.00, 100.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-773-

HOH

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Components

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


Mass: 45968.727 Da / Num. of mol.: 1 / Mutation: F419Y
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.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-92X / 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 418.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C24H22N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.34 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 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: May 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→37.758 Å / Num. obs: 35269 / % possible obs: 99.39 % / Redundancy: 3.1 % / CC1/2: 0.93 / Net I/σ(I): 4.27
Reflection shellResolution: 1.81→1.92 Å / Num. unique obs: 11101 / CC1/2: 0.879

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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: 1.806→37.758 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 1763 5 %
Rwork0.1819 --
obs0.1835 35269 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.806→37.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 32 246 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072981
X-RAY DIFFRACTIONf_angle_d0.8854047
X-RAY DIFFRACTIONf_dihedral_angle_d16.7011757
X-RAY DIFFRACTIONf_chiral_restr0.058441
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.806-1.85480.27691330.23132523X-RAY DIFFRACTION97
1.8548-1.90930.23181340.20912554X-RAY DIFFRACTION99
1.9093-1.9710.23251350.19342565X-RAY DIFFRACTION99
1.971-2.04140.22361340.18652550X-RAY DIFFRACTION99
2.0414-2.12310.21971370.1872593X-RAY DIFFRACTION99
2.1231-2.21970.2491330.19222536X-RAY DIFFRACTION99
2.2197-2.33680.24031360.18472576X-RAY DIFFRACTION100
2.3368-2.48310.23871360.19632606X-RAY DIFFRACTION100
2.4831-2.67480.21911350.19262568X-RAY DIFFRACTION100
2.6748-2.94390.22181360.18942579X-RAY DIFFRACTION100
2.9439-3.36970.20441370.17912609X-RAY DIFFRACTION100
3.3697-4.24450.19391370.16072605X-RAY DIFFRACTION100
4.2445-37.7580.19611400.17282642X-RAY DIFFRACTION100

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