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- PDB-8xue: Crystal structure of AtHPPD-Y191497 complex -

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Basic information

Entry
Database: PDB / ID: 8xue
TitleCrystal structure of AtHPPD-Y191497 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
: / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.218 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-Y191497 complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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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)46,4813
Polymers45,9531
Non-polymers5292
Water1,33374
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9636
Polymers91,9052
Non-polymers1,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3540 Å2
ΔGint-38 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.893, 83.819, 61.674
Angle α, β, γ (deg.)90.00, 100.77, 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 (E. coli)
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-A1LW6 / 3-(4-chlorophenyl)-1-methyl-6-nitro-7-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 469.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16ClN3O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion
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 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.218→37.769 Å / Num. obs: 34638 / % possible obs: 92.4 % / Redundancy: 2.77 % / CC1/2: 0.996 / Net I/σ(I): 9.31
Reflection shellResolution: 2.22→2.35 Å / Num. unique obs: 5487 / CC1/2: 0.881

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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: 2.218→37.769 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 904 5 %
Rwork0.1994 --
obs0.2019 18069 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.218→37.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 34 74 2961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082963
X-RAY DIFFRACTIONf_angle_d0.9554022
X-RAY DIFFRACTIONf_dihedral_angle_d18.2951742
X-RAY DIFFRACTIONf_chiral_restr0.053439
X-RAY DIFFRACTIONf_plane_restr0.006524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2184-2.35740.33371510.26852865X-RAY DIFFRACTION95
2.3574-2.53930.32931510.24882873X-RAY DIFFRACTION95
2.5393-2.79480.27041530.2282894X-RAY DIFFRACTION96
2.7948-3.1990.26541520.21572880X-RAY DIFFRACTION96
3.199-4.02970.21611490.17782840X-RAY DIFFRACTION94
4.0297-80.2241480.17132813X-RAY DIFFRACTION92

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