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- PDB-8x6a: Complex structure of AtHPPD with Y18992 -

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Basic information

Entry
Database: PDB / ID: 8x6a
TitleComplex structure of AtHPPD with Y18992
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibiton / Complex
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
: / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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: Complex structure of AtHPPD with Y18992
Authors: Yang, G.-F. / Lin, H.-Y. / Dong, J.
History
DepositionNov 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: 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)46,4473
Polymers45,9531
Non-polymers4942
Water5,134285
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8946
Polymers91,9052
Non-polymers9894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3310 Å2
ΔGint-12 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.869, 83.882, 62.008
Angle α, β, γ (deg.)90.00, 100.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-823-

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-YFC / 2-[[4-[2-(4-methylphenyl)-2-oxidanylidene-ethyl]-3-oxidanylidene-1,4-benzothiazin-6-yl]-oxidanyl-methylidene]cyclohexane-1,3-dione


Mass: 435.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21NO5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 42.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion
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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.48→30.51 Å / Num. obs: 63969 / % possible obs: 99.5 % / Redundancy: 3.82 % / CC1/2: 0.991 / Net I/σ(I): 10
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 1.7 / Num. unique obs: 20948 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→30.499 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 3150 4.92 %
Rwork0.1874 --
obs0.1882 63969 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→30.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 32 285 3175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062968
X-RAY DIFFRACTIONf_angle_d0.9284024
X-RAY DIFFRACTIONf_dihedral_angle_d10.3771698
X-RAY DIFFRACTIONf_chiral_restr0.08438
X-RAY DIFFRACTIONf_plane_restr0.005525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50160.27951180.2612356X-RAY DIFFRACTION89
1.5016-1.52510.27251350.26712607X-RAY DIFFRACTION99
1.5251-1.55010.23841200.23842676X-RAY DIFFRACTION99
1.5501-1.57680.31121410.24712641X-RAY DIFFRACTION99
1.5768-1.60550.24791350.23212615X-RAY DIFFRACTION100
1.6055-1.63640.23831350.2292680X-RAY DIFFRACTION100
1.6364-1.66980.25131180.21822658X-RAY DIFFRACTION100
1.6698-1.70610.24611280.21262656X-RAY DIFFRACTION100
1.7061-1.74580.21841250.20982656X-RAY DIFFRACTION100
1.7458-1.78940.25461360.2042665X-RAY DIFFRACTION100
1.7894-1.83780.24841250.21622657X-RAY DIFFRACTION100
1.8378-1.89190.21911310.20072659X-RAY DIFFRACTION100
1.8919-1.95290.2191480.19372624X-RAY DIFFRACTION99
1.9529-2.02270.20871450.18752672X-RAY DIFFRACTION100
2.0227-2.10370.19431440.18862629X-RAY DIFFRACTION100
2.1037-2.19940.19281210.18952691X-RAY DIFFRACTION100
2.1994-2.31530.21241500.18512651X-RAY DIFFRACTION100
2.3153-2.46030.20951440.18832658X-RAY DIFFRACTION100
2.4603-2.65020.20191380.192646X-RAY DIFFRACTION100
2.6502-2.91670.20831600.18132655X-RAY DIFFRACTION100
2.9167-3.33830.17761340.17232699X-RAY DIFFRACTION100
3.3383-4.20410.16461350.15592682X-RAY DIFFRACTION100
4.2041-80.18081840.1662686X-RAY DIFFRACTION100

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