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- PDB-8hz9: Crystal structure of AtHPPD-Y181136 complex -

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Basic information

Entry
Database: PDB / ID: 8hz9
TitleCrystal structure of AtHPPD-Y181136 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / Inhibitor
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-O4C / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsDong, J. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of AtHPPD-Y181136 complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionJan 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: 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)46,3393
Polymers45,9531
Non-polymers3862
Water3,009167
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6786
Polymers91,9052
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3320 Å2
ΔGint-11 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.805, 83.826, 61.850
Angle α, β, γ (deg.)90.00, 100.66, 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-O4C / 5-methyl-6-[(2-methyl-3-oxidanylidene-1H-pyrazol-4-yl)carbonyl]-3-propan-2-yl-1,2,3-benzotriazin-4-one


Mass: 327.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.23 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25620 / % possible obs: 98 % / Redundancy: 2.2 % / CC1/2: 0.955 / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.3
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 2698 / CC1/2: 0.849

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.011→30 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 1282 5 %
Rwork0.173 --
obs0.1749 25620 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.011→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 25 169 3124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073035
X-RAY DIFFRACTIONf_angle_d0.8554114
X-RAY DIFFRACTIONf_dihedral_angle_d7.7882434
X-RAY DIFFRACTIONf_chiral_restr0.055448
X-RAY DIFFRACTIONf_plane_restr0.006537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.011-2.09150.25071420.19372698X-RAY DIFFRACTION100
2.0915-2.18660.22111430.18762713X-RAY DIFFRACTION100
2.1866-2.30190.23671400.17432657X-RAY DIFFRACTION100
2.3019-2.44610.24961420.18592707X-RAY DIFFRACTION100
2.4461-2.6350.25011420.18762690X-RAY DIFFRACTION100
2.635-2.90010.21091420.18182698X-RAY DIFFRACTION100
2.9001-3.31960.23111430.17512718X-RAY DIFFRACTION100
3.3196-4.18170.16051430.1582711X-RAY DIFFRACTION100
4.1817-300.20891450.16562746X-RAY DIFFRACTION99

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