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- PDB-7x6n: Crystal structure of AtHPPD-Y191710 complex -

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Basic information

Entry
Database: PDB / ID: 7x6n
TitleCrystal structure of AtHPPD-Y191710 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-A0M / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.691 Å
AuthorsLin, H.-Y. / Dong, J. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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
DepositionMar 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 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 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4583
Polymers45,9531
Non-polymers5052
Water3,999222
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9166
Polymers91,9052
Non-polymers1,0114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.341, 84.107, 62.875
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 45952.727 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
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-A0M / ethyl 5-methyl-4-oxidanylidene-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-phenyl-quinazoline-2-carboxylate


Mass: 446.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
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: BL19U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 43999 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17
Reflection shellResolution: 1.69→1.79 Å / Num. unique obs: 3270 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CQS

7cqs


Resolution: 1.691→44.838 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 2199 5 %
Rwork0.1898 --
obs0.1907 43999 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.691→44.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 34 224 3168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063025
X-RAY DIFFRACTIONf_angle_d0.8334099
X-RAY DIFFRACTIONf_dihedral_angle_d8.5722427
X-RAY DIFFRACTIONf_chiral_restr0.055443
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6913-1.7280.3411320.30552518X-RAY DIFFRACTION96
1.728-1.76820.30031360.2752586X-RAY DIFFRACTION100
1.7682-1.81250.30291370.2612602X-RAY DIFFRACTION100
1.8125-1.86150.26351370.22862590X-RAY DIFFRACTION100
1.8615-1.91620.28981380.22122621X-RAY DIFFRACTION100
1.9162-1.97810.23441380.21242614X-RAY DIFFRACTION100
1.9781-2.04880.24131370.20982627X-RAY DIFFRACTION100
2.0488-2.13080.24461370.19642602X-RAY DIFFRACTION100
2.1308-2.22780.23421370.20162611X-RAY DIFFRACTION100
2.2278-2.34530.22881370.19822615X-RAY DIFFRACTION100
2.3453-2.49220.24121390.20542641X-RAY DIFFRACTION100
2.4922-2.68460.22561370.20452593X-RAY DIFFRACTION100
2.6846-2.95470.22821370.1982619X-RAY DIFFRACTION100
2.9547-3.38210.20581400.18592648X-RAY DIFFRACTION100
3.3821-4.26060.15681380.15842629X-RAY DIFFRACTION100
4.2606-44.8380.17141420.16282684X-RAY DIFFRACTION100

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