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

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Basic information

Entry
Database: PDB / ID: 9qmi
TitlePseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Sulcotrione (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-5BQ / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 Sulcotrione (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)81,7156
Polymers80,9482
Non-polymers7674
Water9,926551
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)163,43012
Polymers161,8954
Non-polymers1,5358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_455x-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)163,43012
Polymers161,8954
Non-polymers1,5358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)149.448, 169.893, 78.509
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
11A-775-

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-5BQ / 2-[2-chloro-4-(methylsulfonyl)benzoyl]cyclohexane-1,3-dione / Sulcotrione


Mass: 328.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H13ClO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
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: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.1→64.32 Å / Num. obs: 58606 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.042 / Rrim(I) all: 0.149 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4493 / CC1/2: 0.917 / Rpim(I) all: 0.356 / Rrim(I) all: 1.276 / % possible all: 100

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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: 2.1→57.66 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 2901 4.98 %
Rwork0.2009 --
obs0.2025 58276 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→57.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 44 551 5905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.592
X-RAY DIFFRACTIONf_dihedral_angle_d20.3572090
X-RAY DIFFRACTIONf_chiral_restr0.065767
X-RAY DIFFRACTIONf_plane_restr0.004979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.37021360.30262574X-RAY DIFFRACTION99
2.13-2.170.32071330.29152604X-RAY DIFFRACTION100
2.17-2.210.29711430.272595X-RAY DIFFRACTION100
2.21-2.250.29451440.25892630X-RAY DIFFRACTION99
2.25-2.30.31461280.24992598X-RAY DIFFRACTION99
2.3-2.350.29781250.24792629X-RAY DIFFRACTION100
2.35-2.40.32611220.24722625X-RAY DIFFRACTION99
2.4-2.460.23861520.2312611X-RAY DIFFRACTION99
2.46-2.530.27141460.23952587X-RAY DIFFRACTION99
2.53-2.60.2721660.22882594X-RAY DIFFRACTION99
2.6-2.690.25711500.22192613X-RAY DIFFRACTION99
2.69-2.780.23911200.20772616X-RAY DIFFRACTION99
2.79-2.90.23491590.20472618X-RAY DIFFRACTION100
2.9-3.030.24971270.20442635X-RAY DIFFRACTION100
3.03-3.190.2291320.20422663X-RAY DIFFRACTION100
3.19-3.390.2361250.19862643X-RAY DIFFRACTION99
3.39-3.650.2451270.18592677X-RAY DIFFRACTION100
3.65-4.020.17721290.16992675X-RAY DIFFRACTION100
4.02-4.60.18231120.15412718X-RAY DIFFRACTION100
4.6-5.790.18391710.16292665X-RAY DIFFRACTION100
5.79-57.660.21441540.19742805X-RAY DIFFRACTION99
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)
11.1931-0.8529-0.2521.10650.27280.81720.0368-0.10160.02360.0281-0.0513-0.08030.0415-0.00830.00850.2914-0.0272-0.02950.2829-0.00710.489526.323818.19717.1455
21.2260.7956-0.23221.0281-0.29270.90670.01390.07990.0386-0.07750.00070.15630.0568-0.0288-0.01270.29250.03130.02660.26350.01780.522348.442124.8681-17.1112
36.28312.2588-6.26731.5881-2.18676.28-0.106-0.19960.0651-0.00830.0583-0.36210.13980.3663-0.01310.3351-0.01840.10890.32970.02090.583538.781518.035318.4081
42.49-0.55611.30651.32640.19142.4415-0.06190.07780.04520.0430.10040.48590.101-0.3928-0.05860.3270.02110.08490.43560.05630.68535.945624.741-18.3268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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