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- PDB-8hym: Crystal structure of AtHPPD-Y18030 complex -

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Basic information

Entry
Database: PDB / ID: 8hym
TitleCrystal structure of AtHPPD-Y18030 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-T8H / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 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-Y18030 complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionJan 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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)46,4083
Polymers45,9531
Non-polymers4552
Water3,549197
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8166
Polymers91,9052
Non-polymers9114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3250 Å2
ΔGint-12 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.689, 84.168, 63.037
Angle α, β, γ (deg.)90.00, 100.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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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-T8H / 3-cyclopentyl-1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 396.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
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: 1.06 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.794→50 Å / Num. obs: 36836 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Net I/σ(I): 32.6
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1798 / CC1/2: 0.922

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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: 1.794→35.566 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1788 4.86 %
Rwork0.1818 --
obs0.1836 36822 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.794→35.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 30 197 3127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073011
X-RAY DIFFRACTIONf_angle_d0.8894084
X-RAY DIFFRACTIONf_dihedral_angle_d8.5082410
X-RAY DIFFRACTIONf_chiral_restr0.058444
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7943-1.84280.34361250.25472485X-RAY DIFFRACTION91
1.8428-1.89710.24911280.22612687X-RAY DIFFRACTION99
1.8971-1.95830.2591420.21692703X-RAY DIFFRACTION99
1.9583-2.02830.23461350.19742659X-RAY DIFFRACTION98
2.0283-2.10950.23451470.19012717X-RAY DIFFRACTION99
2.1095-2.20550.23531500.1942719X-RAY DIFFRACTION100
2.2055-2.32170.22871100.19222714X-RAY DIFFRACTION100
2.3217-2.46710.22211250.19252722X-RAY DIFFRACTION100
2.4671-2.65760.21381500.19942691X-RAY DIFFRACTION99
2.6576-2.92490.23781380.19662729X-RAY DIFFRACTION100
2.9249-3.34790.2351430.18762747X-RAY DIFFRACTION100
3.3479-4.21690.20341610.15842689X-RAY DIFFRACTION99
4.2169-35.5660.18531340.15822772X-RAY DIFFRACTION99

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