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- PDB-7wj8: Complex structure of AtHPPD-PyQ1 -

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Basic information

Entry
Database: PDB / ID: 7wj8
TitleComplex structure of AtHPPD-PyQ1
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-0B8 / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 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 5, 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)46,6423
Polymers45,9531
Non-polymers6902
Water4,864270
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2856
Polymers91,9052
Non-polymers1,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3290 Å2
ΔGint-13 kcal/mol
Surface area28520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.716, 83.806, 62.007
Angle α, β, γ (deg.)90.00, 100.41, 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-0B8 / 2-pyren-1-yloxyethyl 2-[1,5-dimethyl-2,4-bis(oxidanylidene)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazolin-3-yl]ethanoate


Mass: 630.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C37H30N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.31 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35227 / % possible obs: 98.9 % / Redundancy: 3.47 % / CC1/2: 0.973 / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.47
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.222 / Num. unique obs: 2491 / CC1/2: 0.937 / % possible all: 96.9

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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: 7VO8

7vo8


Resolution: 1.805→44.353 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 1762 5 %
Rwork0.1651 --
obs0.1667 35222 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.805→44.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 48 273 3228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063037
X-RAY DIFFRACTIONf_angle_d0.8924120
X-RAY DIFFRACTIONf_dihedral_angle_d8.5492429
X-RAY DIFFRACTIONf_chiral_restr0.055447
X-RAY DIFFRACTIONf_plane_restr0.005534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.85380.24051310.1822491X-RAY DIFFRACTION96
1.8538-1.90840.22571340.17662536X-RAY DIFFRACTION99
1.9084-1.96990.23681350.17122567X-RAY DIFFRACTION99
1.9699-2.04040.21511340.16782550X-RAY DIFFRACTION99
2.0404-2.1220.21761360.16642577X-RAY DIFFRACTION99
2.122-2.21860.18121340.16992549X-RAY DIFFRACTION99
2.2186-2.33560.19951350.16392568X-RAY DIFFRACTION100
2.3356-2.48190.22371380.17392612X-RAY DIFFRACTION100
2.4819-2.67350.21661340.17092560X-RAY DIFFRACTION100
2.6735-2.94250.19141360.1712586X-RAY DIFFRACTION100
2.9425-3.36820.18291380.16552607X-RAY DIFFRACTION100
3.3682-4.2430.18631370.14582612X-RAY DIFFRACTION100
4.243-44.3530.17441400.16712645X-RAY DIFFRACTION100

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