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- PDB-8wpc: Complex structure of AtHPPD with LB553 -

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Basic information

Entry
Database: PDB / ID: 8wpc
TitleComplex structure of AtHPPD with LB553
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / Complex / HPPD
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: 1.797 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 LB553
Authors: Yang, G.-F. / Lin, H.-Y. / Dong, J.
History
DepositionOct 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 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)46,3523
Polymers45,9531
Non-polymers3992
Water3,711206
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7046
Polymers91,9052
Non-polymers7984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3300 Å2
ΔGint-10 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.267, 84.121, 62.783
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

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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-X2T / (2R)-3-[2,4-bis(chloranyl)-3-methyl-phenyl]carbonyl-1-cyclopropyl-2-methyl-4-oxidanyl-2H-pyrrol-5-one


Mass: 340.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15Cl2NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
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: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.797→29.959 Å / Num. obs: 36681 / % possible obs: 99.6 % / Redundancy: 3.43 % / CC1/2: 0.999 / Net I/σ(I): 15.31
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 39349 / CC1/2: 0.954

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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: 1.797→29.959 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 1834 5 %
Rwork0.1892 --
obs0.1905 36681 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.797→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 23 206 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062951
X-RAY DIFFRACTIONf_angle_d0.8324005
X-RAY DIFFRACTIONf_dihedral_angle_d17.5031739
X-RAY DIFFRACTIONf_chiral_restr0.055441
X-RAY DIFFRACTIONf_plane_restr0.005522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.797-1.84550.3061390.26472646X-RAY DIFFRACTION98
1.8455-1.89980.25871390.23422650X-RAY DIFFRACTION100
1.8998-1.96110.27451410.21752664X-RAY DIFFRACTION100
1.9611-2.03120.25071410.21122671X-RAY DIFFRACTION100
2.0312-2.11250.22941400.20522665X-RAY DIFFRACTION100
2.1125-2.20860.23581420.20432701X-RAY DIFFRACTION100
2.2086-2.3250.22111400.19272667X-RAY DIFFRACTION100
2.325-2.47060.21951410.20482676X-RAY DIFFRACTION100
2.4706-2.66120.25421410.2112671X-RAY DIFFRACTION100
2.6612-2.92880.20371420.20372694X-RAY DIFFRACTION100
2.9288-3.35210.23161420.18952708X-RAY DIFFRACTION100
3.3521-4.22150.17931420.16552697X-RAY DIFFRACTION100
4.2215-80.18841440.16342737X-RAY DIFFRACTION100

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