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- PDB-8x68: Complex structure of AtHPPD with YH21002 -

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Basic information

Entry
Database: PDB / ID: 8x68
TitleComplex structure of AtHPPD with YH21002
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibiton / 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: 1.895 Å
AuthorsYang, G.-F. / Lin, H.-Y. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Complex structure of AtHPPD with YH21002
Authors: Yang, G.-F. / Lin, H.-Y. / Dong, J.
History
DepositionNov 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: 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)46,4343
Polymers45,9531
Non-polymers4812
Water1,51384
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8686
Polymers91,9052
Non-polymers9634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3270 Å2
ΔGint-11 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.421, 84.119, 62.930
Angle α, β, γ (deg.)90.00, 100.94, 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-YD2 / 3-(4-fluorophenyl)-1,6-dimethyl-7-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 422.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C23H19FN2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.4 Å3/Da / Density % sol: 43.81 %
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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.895→35.52 Å / Num. obs: 31078 / % possible obs: 97.3 % / Redundancy: 3.36 % / CC1/2: 0.997 / Net I/σ(I): 10.25
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 9617 / CC1/2: 0.952

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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: 1.895→35.52 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1553 5 %
Rwork0.2026 --
obs0.2038 31078 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.895→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 32 84 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082985
X-RAY DIFFRACTIONf_angle_d0.9164049
X-RAY DIFFRACTIONf_dihedral_angle_d17.4881762
X-RAY DIFFRACTIONf_chiral_restr0.056441
X-RAY DIFFRACTIONf_plane_restr0.005527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.895-1.95620.34351370.31492608X-RAY DIFFRACTION96
1.9562-2.02610.31761410.28282673X-RAY DIFFRACTION99
2.0261-2.10720.27341400.25362683X-RAY DIFFRACTION99
2.1072-2.20310.31291420.24152683X-RAY DIFFRACTION99
2.2031-2.31920.25781410.22172669X-RAY DIFFRACTION99
2.3192-2.46450.26141400.2222683X-RAY DIFFRACTION99
2.4645-2.65470.2531420.22412689X-RAY DIFFRACTION99
2.6547-2.92180.23041410.2172698X-RAY DIFFRACTION99
2.9218-3.34430.25091430.21312705X-RAY DIFFRACTION99
3.3443-4.21240.17621420.17622701X-RAY DIFFRACTION99
4.2124-80.19171440.16792733X-RAY DIFFRACTION99

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