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

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Basic information

Entry
Database: PDB / ID: 9qmg
TitlePseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Tefuryltrione (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
: / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 Tefuryltrione (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
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,88712
Polymers161,8954
Non-polymers1,9918
Water4,810267
1
A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

A: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

C: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

C: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,88712
Polymers161,8954
Non-polymers1,9918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area6540 Å2
ΔGint-26 kcal/mol
Surface area54010 Å2
MethodPISA
2
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,88712
Polymers161,8954
Non-polymers1,9918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area6630 Å2
ΔGint-27 kcal/mol
Surface area53670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.190, 169.242, 79.577
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
4-hydroxyphenylpyruvate dioxygenase


Mass: 40473.863 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-A1I7L / Tefuryltrione / 2-[2-chloranyl-4-methylsulfonyl-3-[[(2~{S})-oxolan-2-yl]methoxymethyl]phenyl]carbonylcyclohexane-1,3-dione


Mass: 442.910 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C20H23ClO7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus C9 0.09 M NPS 0.1 M Buffer System 3 8.5 30 % v/v Precipitant Mix 1

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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: 2.7→45.46 Å / Num. obs: 52972 / % possible obs: 96.9 % / Redundancy: 4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.117 / Rrim(I) all: 0.241 / Net I/σ(I): 4
Reflection shellResolution: 2.7→2.78 Å / Rmerge(I) obs: 1.336 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4607 / CC1/2: 0.723 / Rpim(I) all: 0.732 / Rrim(I) all: 1.531

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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: 2.7→45.46 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 2468 4.71 %
Rwork0.2462 --
obs0.2481 52439 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10608 0 120 267 10995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.583
X-RAY DIFFRACTIONf_dihedral_angle_d18.8754256
X-RAY DIFFRACTIONf_chiral_restr0.0631540
X-RAY DIFFRACTIONf_plane_restr0.0051968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.40011330.35512731X-RAY DIFFRACTION94
2.75-2.810.40091370.35592756X-RAY DIFFRACTION96
2.81-2.870.39361420.35112766X-RAY DIFFRACTION96
2.87-2.940.39011540.3272764X-RAY DIFFRACTION96
2.94-3.010.32081440.3152797X-RAY DIFFRACTION97
3.01-3.090.40081330.3132812X-RAY DIFFRACTION97
3.09-3.180.3021670.28732822X-RAY DIFFRACTION97
3.18-3.280.29031300.28042782X-RAY DIFFRACTION97
3.28-3.40.31491390.2772769X-RAY DIFFRACTION96
3.4-3.540.33831290.26082824X-RAY DIFFRACTION97
3.54-3.70.30271470.24932777X-RAY DIFFRACTION96
3.7-3.890.25491320.23452791X-RAY DIFFRACTION96
3.89-4.140.27441250.21042799X-RAY DIFFRACTION96
4.14-4.460.25111640.19992731X-RAY DIFFRACTION95
4.46-4.90.19981360.19142712X-RAY DIFFRACTION94
4.9-5.610.21021300.19682800X-RAY DIFFRACTION96
5.61-7.070.29051050.23642806X-RAY DIFFRACTION95
7.07-45.460.2551210.20712732X-RAY DIFFRACTION92
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)
11.30280.740.41441.16840.0111.43320.04290.1236-0.0911-0.19150.033-0.10080.0764-0.0021-0.12620.80590.0701-0.28810.4765-0.02350.986826.2946-27.97542.6966
21.5292-0.70990.66651.1142-0.15551.38220.0214-0.02930.1102-0.0005-0.04380.1454-0.0736-0.0520.10160.2349-0.0547-0.07790.19380.00410.432147.9821-21.316937.205
31.26490.7732-0.42741.3833-0.12731.11180.04130.0586-0.01040.0615-0.02810.02440.01010.0066-0.02160.8790.0163-0.35430.49110.01771.009749.235914.79412.2661
41.2047-1.1325-0.63451.26630.10720.83710.07-0.029-0.0424-0.0489-0.0402-0.07210.028-0.0309-0.07320.4599-0.0124-0.22050.2471-0.04740.630625.086721.480337.3207
58.61191.53474.84281.58343.13896.73190.0737-0.2456-0.6008-0.12730.0574-0.29230.3950.1783-0.16780.8015-0.1417-0.18930.75020.0961.281839.0292-29.01582.7875
69.0531-2.72842.79823.0813-3.47624.1925-0.00750.3485-0.6036-0.2276-0.12970.46860.5446-0.1257-0.06220.34380.0264-0.14280.51920.09460.835935.2132-22.229637.0677
75.38672.1263-1.43562.6849-1.8553.6101-0.0382-0.10410.23440.1924-0.10820.3209-0.1362-0.2327-0.0120.5905-0.0495-0.19630.64050.08980.976436.558515.74852.0927
82.8857-3.9734-2.32156.11744.46936.15350.20430.17320.7573-0.1665-0.0423-0.5004-0.51550.0617-0.19060.65040.2146-0.24510.56230.01150.77737.777722.478137.5177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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