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- PDB-8i0g: Crystal structure of AtHPPD-Y19543 complex -

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Basic information

Entry
Database: PDB / ID: 8i0g
TitleCrystal structure of AtHPPD-Y19543 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / Inhibitor
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-O6R / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 Å
AuthorsDong, J. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of AtHPPD-Y19543 complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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)46,4053
Polymers45,9531
Non-polymers4522
Water4,414245
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8106
Polymers91,9052
Non-polymers9054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3280 Å2
ΔGint-10 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.098, 84.038, 62.779
Angle α, β, γ (deg.)90.00, 100.57, 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-O6R / 3-[(4-fluorophenyl)methyl]-5-methyl-6-[(2-methyl-3-oxidanylidene-1H-pyrazol-4-yl)carbonyl]-1,2,3-benzotriazin-4-one


Mass: 393.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16FN5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 291 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: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.992→30 Å / Num. obs: 26883 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.046 / Net I/σ(I): 34.8
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1364 / CC1/2: 0.99

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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 / Resolution: 1.992→28.759 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 1344 5 %
Rwork0.1672 --
obs0.1685 26875 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.992→28.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 30 248 3174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073006
X-RAY DIFFRACTIONf_angle_d0.8684074
X-RAY DIFFRACTIONf_dihedral_angle_d8.0922407
X-RAY DIFFRACTIONf_chiral_restr0.055442
X-RAY DIFFRACTIONf_plane_restr0.006533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.992-2.06270.26851290.18962438X-RAY DIFFRACTION96
2.0627-2.14530.23681510.17992562X-RAY DIFFRACTION100
2.1453-2.24290.20261270.18362558X-RAY DIFFRACTION100
2.2429-2.36110.20791450.17342540X-RAY DIFFRACTION100
2.3611-2.50890.2151150.1832561X-RAY DIFFRACTION100
2.5089-2.70250.20251430.17832540X-RAY DIFFRACTION100
2.7025-2.97420.19941540.17862558X-RAY DIFFRACTION100
2.9742-3.4040.21351210.1742560X-RAY DIFFRACTION100
3.404-4.28640.17851290.1442594X-RAY DIFFRACTION100
4.2864-28.7590.14911300.15642620X-RAY DIFFRACTION100

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