5IM5 Protein Binding date Mar 05, 2016
title Crystal Structure Of Designed Two-Component Self-Assembling Icosahedral Cage I53-40
authors Y.A.Liu, D.Cascio, M.R.Sawaya, J.B.Bale, M.J.Collazo, C.Thomas, W. N.P.King, D.Baker, T.O.Yeates
compound source
Molecule: Designed Riboflavin Synthase
Chain: K, M, O, Q, S, A, B, C, D, E, F, G, H, I, J
Fragment: Riboflavin Synthase
Ec: 2.5.1.9
Engineered: Yes
Mutation: Yes
Organism_scientific: Methanocaldococcus Jannaschii (Strain 43067 Dsm 2661 Jal-1 Jcm 10045 Nbrc 100440);
Organism_taxid: 243232
Strain: Atcc 43067 Dsm 2661 Jal-1 Jcm 10045 Nbrc 10
Gene: Ribc, Mj1184
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29b

Molecule: Designed Keto-Hydroxyglutarate-Aldolaseketo-Deox Phosphogluconate Aldolase;
Chain: P, T, N, V, W, U, Y, Z, X, 2, 4, 1, L, R, 3
Fragment: Keto-Hydroxyglutarate-Aldolaseketo-Deoxy-Phospho Aldolase;
Ec: 4.1.3.16
Engineered: Yes
Mutation: Yes

Organism_scientific: Vibrionales Bacterium (Strain Swat-3)
Organism_taxid: 391574
Strain: Swat-3
Gene: Vswat3_13722
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29b
symmetry Space Group: I 2 2 2
R_factor 0.240 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
265.620 279.810 301.330 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.70 Å
ligand
enzyme Transferase E.C.2.5.1.9 BRENDA
Gene VSWAT3
Gene
Ontology
ChainFunctionProcessComponent
S, F, K, E, Q, M, C, A, O, J, B, H, D, I, G


T, N, Y, 2, V, Z, 1, L, W, X, 3, P, 4, R, U


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1683 Kb) [Save to disk]
  • Biological Unit Coordinates (5im5.pdb1.gz) 6641 Kb
  • CSU: Contacts of Structural Units for 5IM5
  • Structure Factors (1935 Kb)
  • Retrieve 5IM5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IM5 from S2C, [Save to disk]
  • Re-refined 5im5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IM5 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 5IM5
  • 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
  • Fold representative 5im5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5im5_O] [5im5_4] [5im5_E] [5im5_Y] [5im5_W] [5im5_1] [5im5_A] [5im5_Q] [5im5_H] [5im5_D] [5im5_P] [5im5_G] [5im5_2] [5im5_F] [5im5_C] [5im5_J] [5im5_S] [5im5_L] [5im5_X] [5im5_K] [5im5_U] [5im5_Z] [5im5_T] [5im5_B] [5im5_I] [5im5_M] [5im5_R] [5im5_3] [5im5_V] [5im5_N] [5im5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5IM5
  • Community annotation for 5IM5 at PDBWiki (http://pdbwiki.org)

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