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- PDB-7cqs: Complex structure of HPPD with Topramezone -

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Basic information

Entry
Database: PDB / ID: 7cqs
TitleComplex structure of HPPD with Topramezone
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-GJL / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsLin, H.Y. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Agrochem / Year: 2022
Title: Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules
Authors: Dong, J. / Dong, J. / Yu, X.H. / Yan, Y.C. / Nan, J.X. / He, B. / Ye, B.Q. / Yang, W.C. / Lin, H.Y. / Yang, G.F.
History
DepositionAug 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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)44,6353
Polymers44,2131
Non-polymers4222
Water3,603200
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2706
Polymers88,4252
Non-polymers8454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3260 Å2
ΔGint-10 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.183, 83.903, 62.798
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-782-

HOH

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Components

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


Mass: 44212.652 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-CO / COBALT (II) ION


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.04 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl pH8.5, 0.1M Bicine pH8.5, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 25%(w/v) MPD, 25%(w/v) PEG1000, 25%(w/v) PEG3350

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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: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→30 Å / Num. obs: 25640 / % possible obs: 96.3 % / Redundancy: 2.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.154 / Num. unique obs: 1312 / CC1/2: 0.971

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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: 6JX9

6jx9


Resolution: 1.998→29.903 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 1287 5.02 %
Rwork0.1808 --
obs0.1826 25629 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→29.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 26 200 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062985
X-RAY DIFFRACTIONf_angle_d0.8034047
X-RAY DIFFRACTIONf_dihedral_angle_d7.8942393
X-RAY DIFFRACTIONf_chiral_restr0.052441
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9982-2.07820.26951520.22312630X-RAY DIFFRACTION95
2.0782-2.17280.24761460.20832733X-RAY DIFFRACTION97
2.1728-2.28730.24691590.19232721X-RAY DIFFRACTION97
2.2873-2.43050.20881260.19562733X-RAY DIFFRACTION97
2.4305-2.61810.22791390.19562736X-RAY DIFFRACTION97
2.6181-2.88130.23571690.19052678X-RAY DIFFRACTION96
2.8813-3.29780.20251290.18452756X-RAY DIFFRACTION97
3.2978-4.15310.2091310.16052693X-RAY DIFFRACTION95
4.1531-29.9030.1891360.1672662X-RAY DIFFRACTION92

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