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

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Basic information

Entry
Database: PDB / ID: 9sla
TitlePseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Topramezone (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
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-GJL / : / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAlshref, F.M. / 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 Topramezone (Mn)
Authors: Alshref, F.M. / Dhingra, S. / Farcas, I.M. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
History
DepositionSep 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 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)81,7846
Polymers80,9482
Non-polymers8374
Water13,529751
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint1 kcal/mol
Surface area29670 Å2
Unit cell
Length a, b, c (Å)79.200, 149.950, 87.763
Angle α, β, γ (deg.)90.000, 106.754, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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) / Strain (production host): BL21(DE3) / 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-GJL / 4-[3-(4,5-dihydro-1,2-oxazol-3-yl)-2-methyl-4-methylsulfonyl-phenyl]carbonyl-2-methyl-1~{H}-pyrazol-3-one


Mass: 363.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 60.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: Morpheus H9, 0.1 M Amino acids, 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: 0.94056 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94056 Å / Relative weight: 1
ReflectionResolution: 1.65→67.63 Å / Num. obs: 117150 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 25.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 13.6
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.194 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5773 / CC1/2: 0.716 / Rpim(I) all: 0.741 / Rrim(I) all: 1.408

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→55.95 Å / SU ML: 0.205 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 5963 5.1 %
Rwork0.1652 111026 -
obs0.1665 116989 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.47 Å2
Refinement stepCycle: LAST / Resolution: 1.65→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 52 751 6143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01655571
X-RAY DIFFRACTIONf_angle_d1.39147527
X-RAY DIFFRACTIONf_chiral_restr0.1219776
X-RAY DIFFRACTIONf_plane_restr0.0118999
X-RAY DIFFRACTIONf_dihedral_angle_d18.5552121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.34241940.34263495X-RAY DIFFRACTION94.2
1.67-1.690.32752120.31383679X-RAY DIFFRACTION99.51
1.69-1.710.30321950.29483667X-RAY DIFFRACTION99.51
1.71-1.730.30541700.27773715X-RAY DIFFRACTION99.59
1.73-1.750.28221870.25863725X-RAY DIFFRACTION99.69
1.75-1.780.27441850.2363676X-RAY DIFFRACTION99.79
1.78-1.80.27112070.22623739X-RAY DIFFRACTION99.77
1.8-1.830.27221800.21123695X-RAY DIFFRACTION99.69
1.83-1.860.24132030.20673664X-RAY DIFFRACTION99.74
1.86-1.890.25152030.19763718X-RAY DIFFRACTION99.77
1.89-1.920.22622060.19223703X-RAY DIFFRACTION99.72
1.92-1.960.2331950.19813670X-RAY DIFFRACTION99.87
1.96-1.990.22071940.19283714X-RAY DIFFRACTION99.97
1.99-2.030.21912020.17953715X-RAY DIFFRACTION99.85
2.03-2.080.20642240.16853661X-RAY DIFFRACTION99.95
2.08-2.130.19151970.1653727X-RAY DIFFRACTION99.95
2.13-2.180.20642160.16033671X-RAY DIFFRACTION100
2.18-2.240.19472020.15983698X-RAY DIFFRACTION99.95
2.24-2.30.18031870.15183714X-RAY DIFFRACTION99.95
2.3-2.380.2062080.15933731X-RAY DIFFRACTION99.97
2.38-2.460.17461960.16173707X-RAY DIFFRACTION100
2.46-2.560.20192010.16523724X-RAY DIFFRACTION100
2.56-2.680.20891980.17073688X-RAY DIFFRACTION99.95
2.68-2.820.19132180.16563720X-RAY DIFFRACTION100
2.82-30.17731870.16453712X-RAY DIFFRACTION99.97
3-3.230.18272140.16253688X-RAY DIFFRACTION100
3.23-3.550.17642010.16133750X-RAY DIFFRACTION100
3.55-4.070.15161720.13543757X-RAY DIFFRACTION100
4.07-5.120.13492160.12613718X-RAY DIFFRACTION99.97
5.13-55.950.19151930.16193785X-RAY DIFFRACTION99.77
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)
10.7421770661820.0278355845461-0.2390711235181.267633485720.7022135110851.36880093320.03001974583010.0333290548303-0.0139699965781-0.000102015436707-0.02176208296830.09040085317330.0432894008694-0.09925966839060.004750544181810.1967288607470.00680438085552-0.002110714946140.2046094656120.01787411832420.187208103387-13.6577991544-26.761464083620.9279607243
21.02512739963-0.1320745121240.3279171613070.970035834214-0.6140803193771.156993638870.001417242068960.0471341090383-0.00124628627310.0885188280704-0.0229894636712-0.0827021206498-0.1697917320660.09293993616940.02762990500260.2790523423570.00148221415869-0.02420321090150.21721448243-0.02313052363250.20826502562921.0249857532-48.431951793521.6960819816
37.84717224945-7.61381359757-3.270172000537.440299173883.703784299366.69439002984-0.10219666158-0.0535491657098-0.1641418136080.104219856753-0.01597761256410.09141991585470.03967083804060.03020375794530.1164836675190.244048244241-0.006685229404840.01925624306220.3227169771270.00992213393750.329567828473-14.2259011961-39.187164096820.4965725092
43.394983464320.988073521313-0.6814519929172.658849397721.16517701435.064342293180.0101482108130.07858078889920.00337193476328-0.0829030065103-0.0695528441613-0.03626775048850.0341281898957-0.107560467020.07517397803980.412783269722-0.0198073192039-0.02604532262450.264271033950.00787520273320.33330978110521.1388259112-35.695271415721.3231489089
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - B6 - 4011
22chain BBC - D6 - 4011
33chain CCE601
44chain DDF601

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