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

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Basic information

Entry
Database: PDB / ID: 9qmn
TitlePseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Manganese
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: 2.05 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 Manganese
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)81,2525
Polymers80,9482
Non-polymers3043
Water7,044391
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)162,50410
Polymers161,8954
Non-polymers6086
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)162,50410
Polymers161,8954
Non-polymers6086
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)149.556, 170.579, 76.024
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-685-

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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Morpheus G9: 0.1 M Carboxylic acids 0.1 M Buffer System 3 8.5 30 % v/v Precipitant Mix 1
PH range: 8.5

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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: 2.05→62.95 Å / Num. obs: 61239 / % possible obs: 99.7 % / Redundancy: 9 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.069 / Rrim(I) all: 0.154 / Net I/σ(I): 6.7
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.316 / Num. unique obs: 4375 / CC1/2: 0.879 / Rpim(I) all: 0.657 / Rrim(I) all: 1.476 / % possible all: 96.7

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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: 2.05→56.75 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 3074 5.06 %
Rwork0.2562 --
obs0.2573 60800 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→56.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5305 0 15 391 5711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.504
X-RAY DIFFRACTIONf_dihedral_angle_d17.0882063
X-RAY DIFFRACTIONf_chiral_restr0.061770
X-RAY DIFFRACTIONf_plane_restr0.004987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.36481420.37662466X-RAY DIFFRACTION95
2.08-2.110.39651470.36312597X-RAY DIFFRACTION99
2.11-2.150.36391280.3482602X-RAY DIFFRACTION99
2.15-2.190.32731300.33052588X-RAY DIFFRACTION99
2.19-2.230.34651240.31032645X-RAY DIFFRACTION99
2.23-2.280.29971330.31072593X-RAY DIFFRACTION99
2.28-2.330.34761480.30342574X-RAY DIFFRACTION99
2.33-2.380.30331460.29252603X-RAY DIFFRACTION99
2.38-2.440.28251570.28412597X-RAY DIFFRACTION99
2.44-2.510.36421330.27582578X-RAY DIFFRACTION99
2.51-2.580.33361490.28422629X-RAY DIFFRACTION99
2.58-2.660.30271580.28262582X-RAY DIFFRACTION99
2.66-2.760.28551200.26692635X-RAY DIFFRACTION99
2.76-2.870.31931480.28352621X-RAY DIFFRACTION99
2.87-30.29231290.26362634X-RAY DIFFRACTION100
3-3.160.29891100.26382687X-RAY DIFFRACTION99
3.16-3.360.28241420.25222628X-RAY DIFFRACTION99
3.36-3.620.25411300.24392660X-RAY DIFFRACTION100
3.62-3.980.2491590.22012639X-RAY DIFFRACTION99
3.98-4.560.2331360.20482688X-RAY DIFFRACTION100
4.56-5.740.21451500.21112685X-RAY DIFFRACTION99
5.74-56.750.24411550.24122795X-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)
11.1246-0.68660.11441.2502-0.290.97720.0003-0.03750.00660.0826-0.0290.2382-0.0393-0.03050.03530.2412-0.0344-0.01840.22940.01420.5581-26.3896-24.979516.8676
20.90250.81480.06061.45310.32491.0373-0.00560.0878-0.0031-0.1344-0.0284-0.1159-0.068-0.00290.03110.24580.0425-0.01610.24620.00790.5512-48.5389-18.4594-17.0073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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