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- EMDB-51698: The structure of ornithine decarboxylase from Leishmania infantum... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51698
TitleThe structure of ornithine decarboxylase from Leishmania infantum in complex with PLP
Map data
Sample
  • Complex: ornithine decarboxylase homodimer with PLP cofactor
    • Protein or peptide: ornithine decarboxylase
Keywordsdecarboxylase pyridoxal 5'-phosphate polyamine biosynthesis Orn/Lys/Arg decarboxylase class-II family / LYASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsFiorillo A / Antonelli A / Ilari A / Tria G
Funding support Italy, 1 items
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, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51698.png

Downloads & links

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Map

FileDownload / File: emd_51698.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.25503743 - 0.4798398
Average (Standard dev.)0.00029411007 (±0.014719301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51698_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51698_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ornithine decarboxylase homodimer with PLP cofactor

EntireName: ornithine decarboxylase homodimer with PLP cofactor
Components
  • Complex: ornithine decarboxylase homodimer with PLP cofactor
    • Protein or peptide: ornithine decarboxylase

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Supramolecule #1: ornithine decarboxylase homodimer with PLP cofactor

SupramoleculeName: ornithine decarboxylase homodimer with PLP cofactor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leishmania infantum (eukaryote)

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Macromolecule #1: ornithine decarboxylase

MacromoleculeName: ornithine decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ornithine decarboxylase
Source (natural)Organism: Leishmania infantum (eukaryote)
Molecular weightTheoretical: 79.800156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MGDHDVALCH VSRYNHANYW AFVPLPTVSD DTGCDSLHHD SASERIRMAP PASASKAGAA EERLHPYER RLLDQYQIHL QPANRNPLSR ADSAAGREET AQTPAQVQMV SGVAVADSTS DQHASVASSQ DLVDLFFLEG S QAVDGLCF ...String:
MGSSHHHHHH SSGLVPRGSH MGDHDVALCH VSRYNHANYW AFVPLPTVSD DTGCDSLHHD SASERIRMAP PASASKAGAA EERLHPYER RLLDQYQIHL QPANRNPLSR ADSAAGREET AQTPAQVQMV SGVAVADSTS DQHASVASSQ DLVDLFFLEG S QAVDGLCF SPYPIYGWRT AEERRAAVCE VFKTYNVVTR LPASPAALAA AQRRYSRHRH SAIAPINKSA IETREQYWRR LS NLYTQKG VKDAASAADA AATTATNGAV PAAPAYEPED PFYIIDLGRV VEQMARWRHE LPMVRPYFAV (LLP)SNPQPAVL EVLSALGAGF DCASKEEIHM VLGRQLVASP DDIIFANPCK QLGDLREAQA CGVTYVTVDN PLEMEKISRL MPSAHAIIRI KTNDSKAQC SFSTKFGAPL EDVEGLLEAA RQFNVTVCGV SFHVGSGNDD QSAYVSAVRD AYQVFQQAVQ YGFKCTILDI G GGFPGTEV VEGSGNTSFE AIARTIRPVL AELFGGGDVT IISEPGRYFT AASHALLMNV FASRTLRLSD VEVSRQAFQS VV SMDEPEE YQYYVNDGLY HSFNCILFDH AHPTLLLLND GDGADGVESG TEAAAVCSEE EGETSLSGPL ANDALFMSAW DRR RSFARR PLRITTIFGP TCDSMDCILK KQPFPEMKLG DWLLVPDMGS YTTAAAGFFN GFATRRLEWV SSVDLCARPR PVYT REGNT LRCVSE

UniProtKB: ornithine decarboxylase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9fos

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100487
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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