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- PDB-8whp: Crystal structure of AtHPPD-YH201042 complex -

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Basic information

Entry
Database: PDB / ID: 8whp
TitleCrystal structure of AtHPPD-YH201042 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / Complex
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: 1.919 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: Crystal structure of AtHPPD-YH201042 complex
Authors: Yang, G.-F. / Lin, H.-Y. / Dong, J.
History
DepositionSep 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)46,4503
Polymers45,9531
Non-polymers4972
Water3,171176
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9006
Polymers91,9052
Non-polymers9954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3570 Å2
ΔGint-36 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.669, 83.815, 61.747
Angle α, β, γ (deg.)90.00, 100.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-637-

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-WI0 / 6-(1,3-dimethyl-5-oxidanyl-pyrazol-4-yl)carbonyl-3-(2-ethoxyethyl)-5-methyl-2-(trifluoromethyl)quinazolin-4-one


Mass: 438.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H21F3N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.31 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 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: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.919→50 Å / Num. obs: 29186 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 1.919→1.986 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2665 / CC1/2: 0.878

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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: 1.919→30.325 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 1460 5 %
Rwork0.1752 --
obs0.1767 29186 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.919→30.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 32 176 3092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072995
X-RAY DIFFRACTIONf_angle_d0.9014065
X-RAY DIFFRACTIONf_dihedral_angle_d17.3831764
X-RAY DIFFRACTIONf_chiral_restr0.054444
X-RAY DIFFRACTIONf_plane_restr0.006529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.919-1.98750.26671400.24712665X-RAY DIFFRACTION96
1.9875-2.06710.28041470.21792793X-RAY DIFFRACTION100
2.0671-2.16110.25631460.20252760X-RAY DIFFRACTION100
2.1611-2.2750.22341460.18542774X-RAY DIFFRACTION100
2.275-2.41750.21911430.17822733X-RAY DIFFRACTION99
2.4175-2.60410.20381480.18562810X-RAY DIFFRACTION100
2.6041-2.86590.20761470.17752787X-RAY DIFFRACTION100
2.8659-3.28020.21541470.17412783X-RAY DIFFRACTION100
3.2802-4.13110.17681460.15432788X-RAY DIFFRACTION100
4.1311-30.3250.18571500.16332833X-RAY DIFFRACTION99

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