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- PDB-9kgm: Complex structure of OsHPPD with MBQ -

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Basic information

Entry
Database: PDB / ID: 9kgm
TitleComplex structure of OsHPPD with MBQ
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / Complex / HPPD
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / metal ion 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-92X / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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 OsHPPD with MBQ
Authors: Yang, G.-F. / Lin, H.-Y. / Dong, J.
History
DepositionNov 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: 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
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9336
Polymers93,9782
Non-polymers9554
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-21 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.676, 153.676, 81.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase


Mass: 46989.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: OSJNBa0085K21.52, P0669G09.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6H4V1
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Co
#3: Chemical ChemComp-92X / 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 418.442 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C24H22N2O5
Has ligand of interestN
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.2M MgCl2, 0.1M HEPES pH 7.0, 20% PEG 6000

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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: 1.799→40.79 Å / Num. obs: 37536 / % possible obs: 98.9 % / Redundancy: 2.12 % / CC1/2: 0.998 / Net I/σ(I): 10.13
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 20964 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→40.79 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2922 1103 4.91 %
Rwork0.2758 --
obs0.2766 22460 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5507 0 64 0 5571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025708
X-RAY DIFFRACTIONf_angle_d0.5677780
X-RAY DIFFRACTIONf_dihedral_angle_d14.881916
X-RAY DIFFRACTIONf_chiral_restr0.04845
X-RAY DIFFRACTIONf_plane_restr0.0041049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.020.39721450.37462615X-RAY DIFFRACTION99
3.02-3.180.3631280.33292601X-RAY DIFFRACTION100
3.18-3.380.35161350.3262635X-RAY DIFFRACTION100
3.38-3.640.39951190.34842650X-RAY DIFFRACTION100
3.64-40.3381500.2992638X-RAY DIFFRACTION100
4-4.580.2741400.25172676X-RAY DIFFRACTION100
4.58-5.770.24221450.23752698X-RAY DIFFRACTION100
5.77-80.24021410.24022844X-RAY DIFFRACTION100

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