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- PDB-7wjj: Complex structure of AtHPPD-PyQ2 -

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Basic information

Entry
Database: PDB / ID: 7wjj
TitleComplex structure of AtHPPD-PyQ2
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / Enzyme
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-0I0 / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 Å
AuthorsYang, G.-F. / Lin, H.-Y. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Agrochem / Year: 2022
Title: Design of an HPPD fluorescent probe and visualization of plant responses to abiotic stress
Authors: Zeng, X. / Huang, Y. / Dong, J. / Ma, X. / Nan, J.X. / Chen, W. / Lin, H.Y. / Yang, W.C. / Liu, X. / Yin, J. / Yang, G.F.
History
DepositionJan 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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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)46,6413
Polymers45,9531
Non-polymers6892
Water5,296294
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2836
Polymers91,9052
Non-polymers1,3774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3380 Å2
ΔGint-12 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.909, 83.885, 62.405
Angle α, β, γ (deg.)90.00, 100.50, 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-0I0 / 2-[1,5-dimethyl-2,4-bis(oxidanylidene)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazolin-3-yl]-N-(2-pyren-1-yloxyethyl)ethanamide


Mass: 629.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H31N3O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.89 %
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: 0.989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 50765 / % possible obs: 99.1 % / Redundancy: 3.43 % / CC1/2: 0.994 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.63
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.518 / Num. unique obs: 3679 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WJ8

7wj8


Resolution: 1.603→44.543 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 2538 5 %
Rwork0.1794 --
obs0.1803 50765 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.603→44.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 48 297 3239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063034
X-RAY DIFFRACTIONf_angle_d0.9564117
X-RAY DIFFRACTIONf_dihedral_angle_d9.0562418
X-RAY DIFFRACTIONf_chiral_restr0.055443
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6034-1.63430.32271310.28482489X-RAY DIFFRACTION93
1.6343-1.66760.25821400.25072669X-RAY DIFFRACTION100
1.6676-1.70390.2721400.23132662X-RAY DIFFRACTION100
1.7039-1.74350.23581420.21742691X-RAY DIFFRACTION100
1.7435-1.78710.20091420.20472703X-RAY DIFFRACTION100
1.7871-1.83550.23341430.19482712X-RAY DIFFRACTION100
1.8355-1.88950.19951390.18592642X-RAY DIFFRACTION100
1.8895-1.95050.21191400.18442680X-RAY DIFFRACTION100
1.9505-2.02020.19771410.18272670X-RAY DIFFRACTION100
2.0202-2.10110.22171420.18422692X-RAY DIFFRACTION100
2.1011-2.19670.20611420.18492708X-RAY DIFFRACTION100
2.1967-2.31250.19041400.17582663X-RAY DIFFRACTION100
2.3125-2.45740.20471420.18292689X-RAY DIFFRACTION100
2.4574-2.64710.22431410.18542692X-RAY DIFFRACTION100
2.6471-2.91340.21361420.18012697X-RAY DIFFRACTION100
2.9134-3.33490.16891430.1692717X-RAY DIFFRACTION100
3.3349-4.20110.15631430.15522703X-RAY DIFFRACTION100
4.2011-44.5430.17941450.16742748X-RAY DIFFRACTION100

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