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- PDB-5ywk: Crystal structure of Arabidopsis thaliana HPPD complexed with Ben... -

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Basic information

Entry
Database: PDB / ID: 5ywk
TitleCrystal structure of Arabidopsis thaliana HPPD complexed with Benquitrione-Methyl
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / 4-hydroxyphenylpyruvate dioxygenase / Herbicide / drug discovery
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 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / 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 ...4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-92X / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsYang, W.C. / Lin, H.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)21672079 China
National Science Foundation (China)21332004 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide.
Authors: Qu, R.Y. / Nan, J.X. / Yan, Y.C. / Chen, Q. / Ndikuryayo, F. / Wei, X.F. / Yang, W.C. / Lin, H.Y. / Yang, G.F.
History
DepositionNov 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)98,7026
Polymers97,7482
Non-polymers9554
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-9 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.753, 95.753, 194.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 48873.832 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
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-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.: 2 / Source method: obtained synthetically / Formula: C24H22N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 291.16 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 33% PEG 400, 0.1M sodium chloride, 0.1M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97881 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 2.804→50 Å / Num. obs: 22388 / % possible obs: 97 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.89
Reflection shellResolution: 2.804→2.904 Å / Redundancy: 13 % / Rmerge(I) obs: 0.242 / Num. unique obs: 1120

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TFZ

1tfz


Resolution: 2.804→38.519 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.41
RfactorNum. reflection% reflection
Rfree0.2946 1153 5.16 %
Rwork0.2467 --
obs0.2493 22348 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.804→38.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 64 2 5756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095891
X-RAY DIFFRACTIONf_angle_d0.7887964
X-RAY DIFFRACTIONf_dihedral_angle_d17.8292109
X-RAY DIFFRACTIONf_chiral_restr0.252869
X-RAY DIFFRACTIONf_plane_restr0.0041023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8036-2.93120.33131310.24982659X-RAY DIFFRACTION99
2.9312-3.08560.33441430.25822663X-RAY DIFFRACTION100
3.0856-3.27890.32121610.27022639X-RAY DIFFRACTION100
3.2789-3.53190.29451500.2452670X-RAY DIFFRACTION99
3.5319-3.8870.27571490.23212621X-RAY DIFFRACTION97
3.887-4.44870.25391300.21652522X-RAY DIFFRACTION93
4.4487-5.60220.22381320.23652578X-RAY DIFFRACTION93
5.6022-38.52310.35951570.27522843X-RAY DIFFRACTION97

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