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- PDB-9gyg: The structure of ornithine decarboxylase from Leishmania infantum... -

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Basic information

Entry
Database: PDB / ID: 9gyg
TitleThe structure of ornithine decarboxylase from Leishmania infantum in complex with PLP
Componentsornithine decarboxylase
KeywordsLYASE / decarboxylase pyridoxal 5'-phosphate polyamine biosynthesis Orn/Lys/Arg decarboxylase class-II family
Function / homology
Function and homology information


ornithine decarboxylase / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
ornithine decarboxylase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsFiorillo, A. / Antonelli, A. / Ilari, A. / Tria, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other governmentRM123188F763A9D5 Italy
CitationJournal: To Be Published
Title: The structure of ornithine decarboxylase from Leishmania infantum in complex with PLP
Authors: Fiorillo, A. / Antonelli, A. / Ilari, A. / Tria, G.
History
DepositionOct 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ornithine decarboxylase
B: ornithine decarboxylase


Theoretical massNumber of molelcules
Total (without water)159,6002
Polymers159,6002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5460 Å2
ΔGint-24 kcal/mol
Surface area34550 Å2
MethodPISA

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Components

#1: Protein ornithine decarboxylase


Mass: 79800.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ.12.0100 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AGB5, ornithine decarboxylase
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ornithine decarboxylase homodimer with PLP cofactor / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Leishmania infantum (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 37 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100487 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 95.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00247382
ELECTRON MICROSCOPYf_angle_d0.483610016
ELECTRON MICROSCOPYf_chiral_restr0.03911096
ELECTRON MICROSCOPYf_plane_restr0.0031294
ELECTRON MICROSCOPYf_dihedral_angle_d4.32461005

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