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- PDB-7x5y: Crystal structure of AtHPPD-Y14240 complex -

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Basic information

Entry
Database: PDB / ID: 7x5y
TitleCrystal structure of AtHPPD-Y14240 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-HZS / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsLin, H.-Y. / Dong, J. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Discovery of Subnanomolar Inhibitors of 4-Hydroxyphenylpyruvate Dioxygenase via Structure-Based Rational Design.
Authors: Dong, J. / Dong, J. / Yu, X.H. / Yan, Y.C. / Nan, J.X. / Ye, B.Q. / Yang, W.C. / Lin, H.Y. / Yang, G.F.
History
DepositionMar 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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)46,5645
Polymers45,9531
Non-polymers6124
Water4,720262
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,12910
Polymers91,9052
Non-polymers1,2238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4670 Å2
ΔGint-63 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.829, 83.961, 62.091
Angle α, β, γ (deg.)90.00, 100.43, 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-HZS / (1R,3S)-5-methyl-2-[(1S)-2-naphthalen-1-yloxy-1-oxidanyl-ethyl]cyclohexane-1,3-diol


Mass: 316.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24O4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.34 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: 0.989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.498→30 Å / Num. obs: 60815 / % possible obs: 98.2 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.2
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2973 / CC1/2: 0.873

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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: 7CQR

7cqr


Resolution: 1.498→28.082 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 3010 4.95 %
Rwork0.1734 --
obs0.1744 60808 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.498→28.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 40 264 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053009
X-RAY DIFFRACTIONf_angle_d0.8124079
X-RAY DIFFRACTIONf_dihedral_angle_d8.1251702
X-RAY DIFFRACTIONf_chiral_restr0.08450
X-RAY DIFFRACTIONf_plane_restr0.005528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4981-1.52150.24661240.23792378X-RAY DIFFRACTION90
1.5215-1.54650.25961210.22122696X-RAY DIFFRACTION99
1.5465-1.57310.24091400.21392654X-RAY DIFFRACTION99
1.5731-1.60170.23211310.20412632X-RAY DIFFRACTION99
1.6017-1.63250.22081410.19582678X-RAY DIFFRACTION99
1.6325-1.66590.22191220.18762658X-RAY DIFFRACTION99
1.6659-1.70210.22911210.18752636X-RAY DIFFRACTION99
1.7021-1.74170.20561340.18582627X-RAY DIFFRACTION97
1.7417-1.78520.2011280.1852528X-RAY DIFFRACTION94
1.7852-1.83350.19781310.18512643X-RAY DIFFRACTION98
1.8335-1.88740.19891180.17832657X-RAY DIFFRACTION100
1.8874-1.94830.18521620.17472646X-RAY DIFFRACTION99
1.9483-2.01790.19241410.17052646X-RAY DIFFRACTION99
2.0179-2.09870.20451390.17782675X-RAY DIFFRACTION99
2.0987-2.19420.18071240.1782680X-RAY DIFFRACTION99
2.1942-2.30980.18431460.17412608X-RAY DIFFRACTION98
2.3098-2.45450.19341410.17882623X-RAY DIFFRACTION97
2.4545-2.64380.19951320.17962548X-RAY DIFFRACTION95
2.6438-2.90970.20171640.1762666X-RAY DIFFRACTION100
2.9097-3.33010.19321320.16732707X-RAY DIFFRACTION100
3.3301-4.19340.16461390.14792666X-RAY DIFFRACTION99
4.1934-28.0820.18091790.16612546X-RAY DIFFRACTION94

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