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- PDB-8i2s: Crystal structure of AtHPPD-Y18979 complex -

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Basic information

Entry
Database: PDB / ID: 8i2s
TitleCrystal structure of AtHPPD-Y18979 complex
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Complex / Inhibitor
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
: / Chem-T4I / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 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-Y18979 complex
Authors: Dong, J. / Lin, H.-Y. / Yang, G.-F.
History
DepositionJan 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: 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)46,5793
Polymers46,0521
Non-polymers5272
Water4,378243
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1596
Polymers92,1042
Non-polymers1,0554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3300 Å2
ΔGint-11 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.052, 83.951, 62.118
Angle α, β, γ (deg.)90.00, 100.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvic acid oxidase / 4HPPD / HPD / HPPDase


Mass: 46051.855 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-T4I / 1,5-dimethyl-3-(naphthalen-2-ylmethyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 468.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
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: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 50656 / % possible obs: 95 % / Redundancy: 2.2 % / CC1/2: 0.998 / Net I/σ(I): 15.87
Reflection shellResolution: 1.59→1.62 Å / Num. unique obs: 2471 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.592→44.518 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 2534 5 %
Rwork0.1886 --
obs0.1896 50656 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.592→44.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 36 243 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063004
X-RAY DIFFRACTIONf_angle_d0.8364077
X-RAY DIFFRACTIONf_dihedral_angle_d8.0512393
X-RAY DIFFRACTIONf_chiral_restr0.056440
X-RAY DIFFRACTIONf_plane_restr0.006531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5923-1.62290.28631300.27762471X-RAY DIFFRACTION91
1.6229-1.65610.29171390.26512637X-RAY DIFFRACTION97
1.6561-1.69210.28651390.24042644X-RAY DIFFRACTION97
1.6921-1.73140.26971410.23422670X-RAY DIFFRACTION97
1.7314-1.77470.21451390.22322647X-RAY DIFFRACTION97
1.7747-1.82270.29731400.22532658X-RAY DIFFRACTION97
1.8227-1.87640.23731400.21412665X-RAY DIFFRACTION98
1.8764-1.93690.24091410.21252669X-RAY DIFFRACTION98
1.9369-2.00620.23371400.20542656X-RAY DIFFRACTION98
2.0062-2.08650.2471410.2082684X-RAY DIFFRACTION98
2.0865-2.18140.24821420.20422686X-RAY DIFFRACTION98
2.1814-2.29640.19321420.19842697X-RAY DIFFRACTION98
2.2964-2.44030.19751400.19812677X-RAY DIFFRACTION98
2.4403-2.62870.21681430.19832716X-RAY DIFFRACTION98
2.6287-2.89320.20781430.19062706X-RAY DIFFRACTION99
2.8932-3.31170.19431440.17892731X-RAY DIFFRACTION99
3.3117-4.1720.17971430.15872726X-RAY DIFFRACTION99
4.172-44.5180.18691470.16642782X-RAY DIFFRACTION99

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