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- PDB-7ezq: Complex structure of AtHPPD with inhibitor Y15832 -

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Basic information

Entry
Database: PDB / ID: 7ezq
TitleComplex structure of AtHPPD with inhibitor Y15832
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsHYDROLASE / Complex / inhibitor
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / 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-0O0 / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.886 Å
AuthorsLin, H.Y. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Complex structure of AtHPPD with inhibitor Y18093
Authors: Lin, H.Y. / Yang, G.F.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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)45,7033
Polymers45,2261
Non-polymers4772
Water3,909217
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4076
Polymers90,4522
Non-polymers9554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3280 Å2
ΔGint-12 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.567, 83.747, 61.636
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

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Components

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


Mass: 45225.891 Da / Num. of mol.: 1
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-0O0 / 6-(1,3-dimethyl-5-oxidanyl-pyrazol-4-yl)carbonyl-1,5-dimethyl-3-(2-methylphenyl)quinazoline-2,4-dione


Mass: 418.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.886→50 Å / Num. obs: 28620 / % possible obs: 94.5 % / Redundancy: 3.4 % / CC1/2: 0.984 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.91
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1404 / CC1/2: 0.722 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M6D

6m6d


Resolution: 1.886→41.873 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1354 4.74 %
Rwork0.1849 --
obs0.1862 28591 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.886→41.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 1 217 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083010
X-RAY DIFFRACTIONf_angle_d0.984083
X-RAY DIFFRACTIONf_dihedral_angle_d22.2971068
X-RAY DIFFRACTIONf_chiral_restr0.073444
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8864-1.95390.26961080.1922246X-RAY DIFFRACTION77
1.9539-2.03210.24451210.192818X-RAY DIFFRACTION96
2.0321-2.12460.24581380.18552783X-RAY DIFFRACTION95
2.1246-2.23660.19461120.18312717X-RAY DIFFRACTION93
2.2366-2.37670.24991390.18642828X-RAY DIFFRACTION96
2.3767-2.56020.23761530.19552819X-RAY DIFFRACTION97
2.5602-2.81780.23491340.1932820X-RAY DIFFRACTION96
2.8178-3.22540.20531590.18752800X-RAY DIFFRACTION96
3.2254-4.06310.18561520.16982744X-RAY DIFFRACTION94
4.0631-41.8730.19261380.18632662X-RAY DIFFRACTION89

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