7ODC Lyase date Mar 03, 1999
title Crystal Structure Ornithine Decarboxylase From Mouse, Trunca Residues From The C-Terminus, To 1.6 Angstrom Resolution
authors A.D.Kern, M.A.Oliveira, P.Coffino, M.L.Hackert
compound source
Molecule: Protein (Ornithine Decarboxylase)
Chain: A
Synonym: Odc, Modc, Modc'
Ec: 4.1.1.17
Engineered: Yes
Mutation: Yes
Other_details: Schiff-Base Linkage Between Plp And K69
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Cell_line: S49.1
Tissue: Lymphoma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Other_details: The Gene Was Cloned From A Balb-C Mouse Lymp Line In Which The Odc Gene Was Amplified By Selection With Cell Line Of Origin Was S49.1, Obtained From The Salk Insti Culture Center In 1974. The Odc- Amplified Lymphoma Cell Li Obtained As A Result Of Selection With Dfmo Was D4. The Gen Been Cloned From Many Mouse Strains Since, And The Orf Is I Among These, So Far As We Know. The Expression Of The Prote E.Coli.
symmetry Space Group: P 21 21 2
R_factor 0.199 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
118.500 74.000 45.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand PLP enzyme Lyase E.C.4.1.1.17 BRENDA
note 7ODC is a representative structure
related structures by homologous chain: 2TOD
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases., Kern AD, Oliveira MA, Coffino P, Hackert ML, Structure Fold Des 1999 May;7(5):567-81. PMID:10378276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (7odc.pdb1.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 7ODC
  • CSU: Contacts of Structural Units for 7ODC
  • Likely Quarternary Molecular Structure file(s) for 7ODC
  • Structure Factors (362 Kb)
  • Retrieve 7ODC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 7ODC from S2C, [Save to disk]
  • Re-refined 7odc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 7ODC in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 7ODC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 7ODC, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d7odca1, region A:2-43,A:284-418 [Jmol] [rasmolscript] [script source]
        - Domain d7odca2, region A:44-283 [Jmol] [rasmolscript] [script source]
  • Fold representative 7odc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [7odc_A] [7odc]
  • SWISS-PROT database: [P00860]
  • Domain organization of [DCOR_MOUSE] by SWISSPFAM
  • Other resources with information on 7ODC
  • Community annotation for 7ODC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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