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- PDB-9qmj: Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex... -

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Basic information

Entry
Database: PDB / ID: 9qmj
TitlePseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Mesotrione (Mn)
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / Phenylalanine catabolism / Tyrosine catabolism / Iron / Metal-binding / 4-hydroxyphenylpyruvate / homogentisic acid
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / metal ion binding
Similarity search - Function
Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal / 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-92L / : / DI(HYDROXYETHYL)ETHER / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlshref, F.M. / Dhingra, S. / Farcas, I.M. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, Saudi Arabia, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Saudi Ministry of EducationDM8000S4747 Saudi Arabia
CitationJournal: To Be Published
Title: Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Mesotrione (Mn)
Authors: Alshref, F.M. / Dhingra, S. / Farcas, I.M. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
History
DepositionMar 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: 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)81,8427
Polymers80,9482
Non-polymers8955
Water13,151730
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,68514
Polymers161,8954
Non-polymers1,78910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
crystal symmetry operation6_445-x-1/2,-y-1/2,z+1/21
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
2
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,68514
Polymers161,8954
Non-polymers1,78910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)149.867, 169.756, 78.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-868-

HOH

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Components

#1: Protein 4-hydroxyphenylpyruvate dioxygenase


Mass: 40473.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing residues were unstructured / Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: hppD, BL240_15045, IR015_07290 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: A0A1L5PRA6, 4-hydroxyphenylpyruvate dioxygenase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-92L / 2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione / Mesotrione


Mass: 339.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13NO7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus A6 0.06 M Divalents 0.1 M Buffer System 2 7.5 30 % v/v Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.9→56.18 Å / Num. obs: 79020 / % possible obs: 99.7 % / Redundancy: 9.6 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.045 / Rrim(I) all: 0.148 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4488 / CC1/2: 0.816 / Rpim(I) all: 0.49 / Rrim(I) all: 1.61 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→56.17 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 3947 5.02 %
Rwork0.2061 --
obs0.2078 78553 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→56.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 55 730 6101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.136
X-RAY DIFFRACTIONf_dihedral_angle_d20.3432113
X-RAY DIFFRACTIONf_chiral_restr0.098771
X-RAY DIFFRACTIONf_plane_restr0.009995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.40121460.36942627X-RAY DIFFRACTION98
1.92-1.950.33331340.34732618X-RAY DIFFRACTION99
1.95-1.970.35251440.32832615X-RAY DIFFRACTION99
1.97-20.36311410.30912646X-RAY DIFFRACTION99
2-2.030.32171450.28812629X-RAY DIFFRACTION99
2.03-2.060.34821510.27722645X-RAY DIFFRACTION99
2.06-2.090.2821570.26312631X-RAY DIFFRACTION99
2.09-2.130.29281420.25382649X-RAY DIFFRACTION100
2.13-2.160.30351460.24052610X-RAY DIFFRACTION100
2.16-2.20.27311440.23952678X-RAY DIFFRACTION99
2.2-2.240.23061260.2422651X-RAY DIFFRACTION100
2.24-2.290.27791240.2192667X-RAY DIFFRACTION99
2.29-2.340.2551350.2212688X-RAY DIFFRACTION99
2.34-2.390.31491480.22032531X-RAY DIFFRACTION96
2.39-2.450.2551570.21042674X-RAY DIFFRACTION99
2.45-2.520.24531440.21062650X-RAY DIFFRACTION99
2.52-2.590.23781410.20222652X-RAY DIFFRACTION99
2.59-2.680.24591320.21062654X-RAY DIFFRACTION99
2.68-2.770.25851420.20532678X-RAY DIFFRACTION99
2.77-2.880.22981430.2012686X-RAY DIFFRACTION100
2.88-3.020.24521270.19582684X-RAY DIFFRACTION99
3.02-3.170.23431370.19412694X-RAY DIFFRACTION100
3.17-3.370.22051540.18622681X-RAY DIFFRACTION100
3.37-3.630.2031470.1832719X-RAY DIFFRACTION100
3.63-40.17091170.16772705X-RAY DIFFRACTION99
4-4.580.17891410.15632664X-RAY DIFFRACTION97
4.58-5.770.18911320.16952761X-RAY DIFFRACTION99
5.77-56.170.25671500.21322819X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.279-0.73510.14611.0187-0.31120.8691-0.0047-0.0997-0.04290.07530.00850.1687-0.0425-0.033-0.00930.2317-0.02370.02470.21910.01440.4255-26.3272-24.855817.1413
21.68470.96970.04071.41920.24110.91330.00670.0981-0.0589-0.0255-0.0162-0.1214-0.0540.00780.01310.20650.0219-0.03510.21020.00010.3199-48.525-18.0796-17.262
37.9825-0.68165.68215.0649-1.51294.25550.0653-0.1487-0.3627-0.0520.15620.31060.1711-0.3276-0.21770.27660.02530.00080.4404-0.03140.4714-38.7443-24.759518.2431
49.50324.2764.57426.22715.56626.2501-0.12830.1073-0.0671-0.010.0754-0.1393-0.03130.1969-00.2964-0.0831-0.1470.3074-0.01880.4345-36.1827-18.0164-18.3226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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