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- PDB-7vo8: Structure of AtHPPD complexed with LSY-1 -

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Basic information

Entry
Database: PDB / ID: 7vo8
TitleStructure of AtHPPD complexed with LSY-1
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-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
Chem-7RQ / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYang, G.-F. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant Physiol. / Year: 2022
Title: In vivo diagnostics of abiotic plant stress responses via in situ real-time fluorescence imaging
Authors: Fu, Y.X. / Liu, S.Y. / Guo, W.Y. / Dong, J. / Nan, J.X. / Lin, H.Y. / Mei, L.C. / Yang, W.C. / Yang, G.F.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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)45,2933
Polymers44,5561
Non-polymers7372
Water3,945219
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5866
Polymers89,1122
Non-polymers1,4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3240 Å2
ΔGint-13 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.978, 84.192, 62.216
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

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Components

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


Mass: 44556.090 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-7RQ / N-[6-[[9-(dimethylamino)-12H-benzo[a]phenoxazin-5-yl]amino]hexyl]-4-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-[oxidanyl(oxidanylidene)-$l^4-azanyl]benzamide


Mass: 677.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C38H39N5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
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: 1.01 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 38475 / % possible obs: 97.8 % / Redundancy: 4.1 % / CC1/2: 0.934 / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.4
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.313 / Num. unique obs: 1983 / CC1/2: 0.962 / % possible all: 99

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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
Starting model: 6JX9

6jx9


Resolution: 1.75→28.173 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 1932 5.02 %
Rwork0.1683 --
obs0.1692 38466 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→28.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 51 219 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063041
X-RAY DIFFRACTIONf_angle_d0.9884124
X-RAY DIFFRACTIONf_dihedral_angle_d8.8282419
X-RAY DIFFRACTIONf_chiral_restr0.058447
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.7940.22291160.18762574X-RAY DIFFRACTION97
1.794-1.84250.21071440.19052671X-RAY DIFFRACTION99
1.8425-1.89670.24291240.17652623X-RAY DIFFRACTION99
1.8967-1.95790.18811350.17542627X-RAY DIFFRACTION99
1.9579-2.02780.17891350.17422644X-RAY DIFFRACTION99
2.0278-2.1090.22461390.17692594X-RAY DIFFRACTION97
2.109-2.20490.2171550.17682556X-RAY DIFFRACTION97
2.2049-2.32110.18351490.1682617X-RAY DIFFRACTION99
2.3211-2.46650.18241600.17692627X-RAY DIFFRACTION99
2.4665-2.65680.1871180.17772638X-RAY DIFFRACTION98
2.6568-2.92390.18331420.17292602X-RAY DIFFRACTION98
2.9239-3.34640.21351530.17152558X-RAY DIFFRACTION96
3.3464-4.21390.151330.15012640X-RAY DIFFRACTION98
4.2139-28.1730.17261290.16412563X-RAY DIFFRACTION94

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