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- PDB-7x8d: Crystal structure of AtHPPD-phenylpyruvate complex -

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Basic information

Entry
Database: PDB / ID: 7x8d
TitleCrystal structure of AtHPPD-phenylpyruvate complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / complex / substrate
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
: / 3-PHENYLPYRUVIC ACID / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsDong, J. / Lin, 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
DepositionMar 12, 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 1.3Oct 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)46,1763
Polymers45,9531
Non-polymers2232
Water3,315184
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3526
Polymers91,9052
Non-polymers4464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4520 Å2
ΔGint-29 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.969, 84.180, 62.075
Angle α, β, γ (deg.)90.00, 100.10, 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-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 42.78 %
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: 1.06 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.695→50 Å / Num. obs: 42939 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.5
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.423 / Num. unique obs: 2129 / CC1/2: 0.883

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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: 7CQS

7cqs


Resolution: 1.695→44.399 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 2106 4.91 %
Rwork0.1908 --
obs0.1924 42921 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.695→44.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 13 185 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062972
X-RAY DIFFRACTIONf_angle_d0.8224030
X-RAY DIFFRACTIONf_dihedral_angle_d8.0872368
X-RAY DIFFRACTIONf_chiral_restr0.053442
X-RAY DIFFRACTIONf_plane_restr0.005530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6951-1.73450.29441230.28242539X-RAY DIFFRACTION92
1.7345-1.77790.29861260.26262730X-RAY DIFFRACTION99
1.7779-1.8260.28011490.23622705X-RAY DIFFRACTION100
1.826-1.87970.25071500.21762718X-RAY DIFFRACTION100
1.8797-1.94040.22391440.20932714X-RAY DIFFRACTION100
1.9404-2.00980.22551360.20082739X-RAY DIFFRACTION100
2.0098-2.09020.26091450.20632713X-RAY DIFFRACTION100
2.0902-2.18530.26031510.21082724X-RAY DIFFRACTION100
2.1853-2.30060.24731460.19842711X-RAY DIFFRACTION100
2.3006-2.44470.22161450.2032718X-RAY DIFFRACTION100
2.4447-2.63340.24121600.2082727X-RAY DIFFRACTION100
2.6334-2.89840.24121470.19892741X-RAY DIFFRACTION100
2.8984-3.31770.20981360.18962759X-RAY DIFFRACTION100
3.3177-4.17940.19681230.16322765X-RAY DIFFRACTION100
4.1794-44.3990.19071250.16982812X-RAY DIFFRACTION100

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