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- PDB-6jx9: Structure of Y17107 complexed HPPD -

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Basic information

Entry
Database: PDB / ID: 6jx9
TitleStructure of Y17107 complexed HPPD
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / complex / dioxygenase
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 / 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-CQC / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLin, H.Y. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: J.Agric.Food Chem. / Year: 2019
Title: Pyrazole-Isoindoline-1,3-dione Hybrid: A Promising Scaffold for 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors.
Authors: He, B. / Dong, J. / Lin, H.Y. / Wang, M.Y. / Li, X.K. / Zheng, B.F. / Chen, Q. / Hao, G.F. / Yang, W.C. / Yang, G.F.
History
DepositionApr 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3083
Polymers48,8741
Non-polymers4342
Water3,315184
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6166
Polymers97,7482
Non-polymers8694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3540 Å2
ΔGint-39 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.939, 84.367, 62.115
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

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Components

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


Mass: 48873.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD / Production host: Escherichia coli (E. coli)
References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-CQC / 5-[(~{Z})-(1,3-dimethyl-5-oxidanylidene-pyrazol-4-ylidene)-oxidanyl-methyl]-2-(phenylmethyl)isoindole-1,3-dione


Mass: 375.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N3O4
#3: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.4 %
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: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 33841 / % possible obs: 93.5 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rsym value: 0.045 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.495 / Num. unique obs: 1759 / CC1/2: 0.909 / Rpim(I) all: 0.263 / % possible all: 96.3

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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: 5YWG

5ywg


Resolution: 1.8→28.489 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2244 1695 5.01 %
Rwork0.1937 --
obs0.1952 33816 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 29 184 3090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072984
X-RAY DIFFRACTIONf_angle_d0.8454045
X-RAY DIFFRACTIONf_dihedral_angle_d23.4861066
X-RAY DIFFRACTIONf_chiral_restr0.056441
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.85090.32241390.25882631X-RAY DIFFRACTION92
1.8509-1.91060.30331350.22912790X-RAY DIFFRACTION96
1.9106-1.97890.2481360.21262804X-RAY DIFFRACTION97
1.9789-2.05810.23451390.19952733X-RAY DIFFRACTION97
2.0581-2.15170.25331420.20372631X-RAY DIFFRACTION92
2.1517-2.26510.24211380.20452733X-RAY DIFFRACTION95
2.2651-2.4070.22831520.19912753X-RAY DIFFRACTION96
2.407-2.59270.25041460.21072732X-RAY DIFFRACTION95
2.5927-2.85340.2331540.20222706X-RAY DIFFRACTION94
2.8534-3.26580.25961400.19572558X-RAY DIFFRACTION89
3.2658-4.11260.18961510.17672659X-RAY DIFFRACTION92
4.1126-28.49260.19721230.17972391X-RAY DIFFRACTION81

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