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- PDB-8hx4: Crystal structure of AtHPPD-Y18549 complex -

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Basic information

Entry
Database: PDB / ID: 8hx4
TitleCrystal structure of AtHPPD-Y18549 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-NQX / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 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-Y18549 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 1.1Oct 23, 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)46,5704
Polymers45,9531
Non-polymers6183
Water4,468248
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1418
Polymers91,9052
Non-polymers1,2356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4010 Å2
ΔGint-40 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.645, 83.528, 62.002
Angle α, β, γ (deg.)90.00, 100.32, 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-NQX / 6-[(R)-[(2R,6R)-2,6-bis(oxidanyl)cyclohexyl]-oxidanyl-methyl]-3-(4,6-dimethylpyrimidin-2-yl)-1,5-dimethyl-quinazoline-2,4-dione


Mass: 440.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N4O5
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
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: Aug 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.896→50 Å / Num. obs: 28847 / % possible obs: 96.2 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.3
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 1441 / CC1/2: 0.8

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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: 1.896→28.416 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 1414 4.9 %
Rwork0.1738 --
obs0.1755 28837 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.896→28.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 41 252 3189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073016
X-RAY DIFFRACTIONf_angle_d0.9114092
X-RAY DIFFRACTIONf_dihedral_angle_d7.9022408
X-RAY DIFFRACTIONf_chiral_restr0.063451
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.896-1.96370.26041110.21622320X-RAY DIFFRACTION80
1.9637-2.04230.2531330.19882801X-RAY DIFFRACTION97
2.0423-2.13520.22811330.18852801X-RAY DIFFRACTION96
2.1352-2.24780.24171320.17562677X-RAY DIFFRACTION93
2.2478-2.38850.22491460.16982835X-RAY DIFFRACTION98
2.3885-2.57280.22721440.17342825X-RAY DIFFRACTION98
2.5728-2.83150.22451410.17272742X-RAY DIFFRACTION94
2.8315-3.24080.19181420.17352834X-RAY DIFFRACTION98
3.2408-4.08110.17811860.15612773X-RAY DIFFRACTION96
4.0811-28.4160.20221460.17612815X-RAY DIFFRACTION95

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