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- PDB-7x5r: Crystal structure of AtHPPD-Lancotrione complex -

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Basic information

Entry
Database: PDB / ID: 7x5r
TitleCrystal structure of AtHPPD-Lancotrione complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / inhibitor / complex
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 / 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-9P5 / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 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 5, 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)46,8626
Polymers45,9531
Non-polymers9095
Water5,008278
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,72412
Polymers91,9052
Non-polymers1,81910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5440 Å2
ΔGint-57 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.555, 83.558, 61.658
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-9P5 / (1R,3R)-2-[(S)-[2-chloranyl-3-[2-(1,3-dioxolan-2-yl)ethoxy]-4-methylsulfonyl-phenyl]-oxidanyl-methyl]cyclohexane-1,3-diol


Mass: 450.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27ClO8S
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.63 %
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: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.644→50 Å / Num. obs: 46072 / % possible obs: 99.7 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.9
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.441 / Num. unique obs: 2346 / CC1/2: 0.877

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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: 1.644→21.663 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 2288 4.97 %
Rwork0.1743 --
obs0.1759 46066 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.644→21.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 57 281 3252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063046
X-RAY DIFFRACTIONf_angle_d1.0734127
X-RAY DIFFRACTIONf_dihedral_angle_d9.0892446
X-RAY DIFFRACTIONf_chiral_restr0.067456
X-RAY DIFFRACTIONf_plane_restr0.006532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.644-1.67950.23581160.21212646X-RAY DIFFRACTION95
1.6795-1.71850.2541520.21252743X-RAY DIFFRACTION100
1.7185-1.76150.24251490.19712717X-RAY DIFFRACTION100
1.7615-1.80910.21521260.19762744X-RAY DIFFRACTION100
1.8091-1.86230.22111290.19462752X-RAY DIFFRACTION100
1.8623-1.92240.2141500.19092719X-RAY DIFFRACTION99
1.9224-1.9910.23231530.17992686X-RAY DIFFRACTION99
1.991-2.07070.22311360.17942779X-RAY DIFFRACTION100
2.0707-2.16480.22291530.17872713X-RAY DIFFRACTION100
2.1648-2.27890.20081500.17242759X-RAY DIFFRACTION100
2.2789-2.42150.19821280.1782731X-RAY DIFFRACTION100
2.4215-2.60810.20651540.18792749X-RAY DIFFRACTION100
2.6081-2.87010.2321450.17472735X-RAY DIFFRACTION100
2.8701-3.28410.18971350.17192773X-RAY DIFFRACTION100
3.2841-4.1330.18641640.14672742X-RAY DIFFRACTION100
4.133-21.6630.19011480.16562790X-RAY DIFFRACTION99

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