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- PDB-8j3c: Crystal structure of AtHPPD-Y19623 complex -

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Basic information

Entry
Database: PDB / ID: 8j3c
TitleCrystal structure of AtHPPD-Y19623 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
: / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsDong, J. / Yang, G.-F. / Lin, H.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of AtHPPD-Y19623 complex
Authors: Dong, J. / Yang, G.-F. / Lin, H.-Y.
History
DepositionApr 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3863
Polymers45,9531
Non-polymers4332
Water4,017223
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7726
Polymers91,9052
Non-polymers8674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3280 Å2
ΔGint-12 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.107, 83.988, 62.283
Angle α, β, γ (deg.)90.00, 100.51, 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-SZO / 5-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-phenyl-quinazolin-4-one


Mass: 374.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
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: BL10U2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 42603 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.11
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 2618 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.703→34.633 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2131 5 %
Rwork0.183 --
obs0.1841 42603 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.703→34.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 29 224 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062997
X-RAY DIFFRACTIONf_angle_d0.8854060
X-RAY DIFFRACTIONf_dihedral_angle_d181772
X-RAY DIFFRACTIONf_chiral_restr0.057441
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.703-1.74250.27661380.25512618X-RAY DIFFRACTION97
1.7425-1.78610.26881430.24022710X-RAY DIFFRACTION100
1.7861-1.83440.23521440.22492721X-RAY DIFFRACTION100
1.8344-1.88830.22851400.21422667X-RAY DIFFRACTION100
1.8883-1.94930.2321410.19762672X-RAY DIFFRACTION100
1.9493-2.01890.19811410.19592683X-RAY DIFFRACTION100
2.0189-2.09980.22321430.19192723X-RAY DIFFRACTION100
2.0998-2.19530.23781430.20062719X-RAY DIFFRACTION100
2.1953-2.3110.20971400.19392656X-RAY DIFFRACTION100
2.311-2.45580.22041430.19872706X-RAY DIFFRACTION100
2.4558-2.64540.21611420.19752696X-RAY DIFFRACTION100
2.6454-2.91140.2381420.1912713X-RAY DIFFRACTION100
2.9114-3.33240.1951440.17932721X-RAY DIFFRACTION100
3.3324-4.19740.15851430.15642715X-RAY DIFFRACTION100
4.1974-34.6330.19621440.16092752X-RAY DIFFRACTION100

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