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- PDB-8hx2: Crystal structure of AtHPPD-Y18405 complex -

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Basic information

Entry
Database: PDB / ID: 8hx2
TitleCrystal structure of AtHPPD-Y18405 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-NQC / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 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-Y18405 complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionJan 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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)46,4773
Polymers45,9531
Non-polymers5242
Water4,486249
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9536
Polymers91,9052
Non-polymers1,0484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3270 Å2
ΔGint-13 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.037, 83.810, 62.397
Angle α, β, γ (deg.)90.00, 100.33, 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-NQC / 3-[2-(3-chlorophenyl)ethyl]-1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexa-1,3-dien-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 464.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21ClN2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
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: 1.06 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.996→30 Å / Num. obs: 26100 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1258 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.996→26.266 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1277 4.89 %
Rwork0.1712 --
obs0.1729 26090 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.996→26.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 34 251 3178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063005
X-RAY DIFFRACTIONf_angle_d0.8244076
X-RAY DIFFRACTIONf_dihedral_angle_d8.052404
X-RAY DIFFRACTIONf_chiral_restr0.052443
X-RAY DIFFRACTIONf_plane_restr0.005531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9964-2.07630.24131150.19222550X-RAY DIFFRACTION90
2.0763-2.17070.24051290.18812672X-RAY DIFFRACTION97
2.1707-2.28510.2451430.18242793X-RAY DIFFRACTION99
2.2851-2.42820.21851370.17982784X-RAY DIFFRACTION100
2.4282-2.61550.21731510.17722799X-RAY DIFFRACTION100
2.6155-2.87840.21291530.1832769X-RAY DIFFRACTION100
2.8784-3.29420.21571390.17872811X-RAY DIFFRACTION100
3.2942-4.14770.19911600.15512784X-RAY DIFFRACTION100
4.1477-26.2660.17551500.162851X-RAY DIFFRACTION99

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