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- PDB-7x8h: Crystal structure of AtHPPD-(+)-Usnic acid complex -

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Basic information

Entry
Database: PDB / ID: 7x8h
TitleCrystal structure of AtHPPD-(+)-Usnic acid 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
Chem-AIY / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.986 Å
AuthorsDong, J. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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 13, 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 30, 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)46,3563
Polymers45,9531
Non-polymers4032
Water2,288127
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7126
Polymers91,9052
Non-polymers8064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3310 Å2
ΔGint-12 kcal/mol
Surface area29220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.608, 83.973, 61.543
Angle α, β, γ (deg.)90.00, 101.99, 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-AIY / (9bR)-2,6-diethanoyl-8,9b-dimethyl-3,7,9-tris(oxidanyl)dibenzofuran-1-one / (+)-Usnic acid / (+)-Usniacin


Mass: 344.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H16O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
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: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.986→30 Å / Num. obs: 25936 / % possible obs: 99.1 % / Redundancy: 6.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.462 / Num. unique obs: 1268 / CC1/2: 0.914

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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: 1.986→29.206 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 1276 4.92 %
Rwork0.1678 --
obs0.1694 25933 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.986→29.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 26 128 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083002
X-RAY DIFFRACTIONf_angle_d1.1254075
X-RAY DIFFRACTIONf_dihedral_angle_d7.8282407
X-RAY DIFFRACTIONf_chiral_restr0.106451
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9862-2.06570.23551350.19592562X-RAY DIFFRACTION93
2.0657-2.15970.23521440.19232763X-RAY DIFFRACTION99
2.1597-2.27350.25261380.17992748X-RAY DIFFRACTION99
2.2735-2.41590.22891490.17532708X-RAY DIFFRACTION99
2.4159-2.60230.22881360.17872786X-RAY DIFFRACTION100
2.6023-2.8640.23321680.18052726X-RAY DIFFRACTION99
2.864-3.27790.19221220.17332773X-RAY DIFFRACTION99
3.2779-4.12790.17631600.15312770X-RAY DIFFRACTION99
4.1279-29.2060.18811240.16032821X-RAY DIFFRACTION99

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