1JDI Isomerase date Jun 13, 2001
title Crystal Structure Of L-Ribulose-5-Phosphate 4-Epimerase
authors Y.Luo, J.Samuel, S.C.Mosimann, J.E.Lee, M.E.Tanner, N.C.J.Strynad
compound source
Molecule: L-Ribulose 5 Phosphate 4-Epimerase
Chain: A, B, C, D, E, F
Ec: 5.1.3.4
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Arad
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Y1090
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pre1
symmetry Space Group: P 4 21 2
R_factor 0.208 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.900 105.900 274.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ZN enzyme Isomerase E.C.5.1.3.4 BRENDA
related structures by homologous chain: 1K0W
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceThe structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization., Luo Y, Samuel J, Mosimann SC, Lee JE, Tanner ME, Strynadka NC, Biochemistry 2001 Dec 11;40(49):14763-71. PMID:11732895
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk]
  • Biological Unit Coordinates (1jdi.pdb1.gz) 143 Kb
  • Biological Unit Coordinates (1jdi.pdb2.gz) 145 Kb
  • Biological Unit Coordinates (1jdi.pdb3.gz) 146 Kb
  • Biological Unit Coordinates (1jdi.pdb4.gz) 146 Kb
  • Biological Unit Coordinates (1jdi.pdb5.gz) 142 Kb
  • Biological Unit Coordinates (1jdi.pdb6.gz) 138 Kb
  • Biological Unit Coordinates (1jdi.pdb7.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 1JDI
  • CSU: Contacts of Structural Units for 1JDI
  • Likely Quarternary Molecular Structure file(s) for 1JDI
  • Structure Factors (614 Kb)
  • Retrieve 1JDI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JDI from S2C, [Save to disk]
  • Re-refined 1jdi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JDI 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 1JDI
  • 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
  • 3D motif for 1JDI, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jdia_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1jdib_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1jdic_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1jdid_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1jdie_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1jdif_, region F [Jmol] [rasmolscript] [script source]
  • 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: [1jdi_D] [1jdi_B] [1jdi] [1jdi_A] [1jdi_F] [1jdi_E] [1jdi_C]
  • SWISS-PROT database: [P08203]
  • Domain organization of [ARAD_ECOLI] by SWISSPFAM
  • Domain found in 1JDI: [Aldolase_II ] by SMART
  • Other resources with information on 1JDI
  • Community annotation for 1JDI 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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