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- PDB-7x5s: Crystal structure of AtHPPD-Y14157 complex -

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Basic information

Entry
Database: PDB / ID: 7x5s
TitleCrystal structure of AtHPPD-Y14157 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-9QL / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.706 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

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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)46,4183
Polymers45,9531
Non-polymers4652
Water2,738152
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8366
Polymers91,9052
Non-polymers9314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.194, 84.211, 62.616
Angle α, β, γ (deg.)90.00, 100.78, 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-9QL / 2-methyl-4-(2-nitro-4-piperidin-1-yl-phenyl)carbonyl-5-phenyl-1H-pyrazol-3-one


Mass: 406.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.46 %
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: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 38655 / % possible obs: 90.5 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1946 / CC1/2: 0.917

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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: 1.706→28.728 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1890 4.89 %
Rwork0.198 --
obs0.1995 38628 90.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.706→28.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 31 153 3044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062969
X-RAY DIFFRACTIONf_angle_d0.8464026
X-RAY DIFFRACTIONf_dihedral_angle_d8.3022372
X-RAY DIFFRACTIONf_chiral_restr0.054441
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.706-1.74850.35091370.29692450X-RAY DIFFRACTION84
1.7485-1.79580.32331170.27312408X-RAY DIFFRACTION82
1.7958-1.84860.27811320.24222721X-RAY DIFFRACTION94
1.8486-1.90830.26821390.22142760X-RAY DIFFRACTION95
1.9083-1.97650.2431290.20692749X-RAY DIFFRACTION95
1.9765-2.05560.23191370.20612743X-RAY DIFFRACTION95
2.0556-2.14910.23581460.20572737X-RAY DIFFRACTION94
2.1491-2.26240.24611280.20042718X-RAY DIFFRACTION93
2.2624-2.40410.24041270.1962629X-RAY DIFFRACTION90
2.4041-2.58960.25481280.20622363X-RAY DIFFRACTION82
2.5896-2.850.25331380.20912766X-RAY DIFFRACTION94
2.85-3.26190.24881520.20292706X-RAY DIFFRACTION94
3.2619-4.10770.18241420.17982579X-RAY DIFFRACTION88
4.1077-28.7280.20281380.17742409X-RAY DIFFRACTION82

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