5IM4 Protein Binding date Mar 05, 2016
title Crystal Structure Of Designed Two-Component Self-Assembling Icosahedral Cage I52-32
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: 6,7-Dimethyl-8-Ribityllumazine Synthase
Chain: A, E, C, B, D, K, L, N, M, O, U, V, X, W, Y, e, f, h
Fragment: 6,7-Dimethyl-8-Ribityllumazine Synthase Residues
Synonym: Dmrl Synthase
Ec: 2.5.1.78
Engineered: Yes
Mutation: Yes
Organism_scientific: Candida Albicans P37005
Organism_taxid: 1094985
Gene: Meu_00538
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Phosphotransferase System, Mannosefructose-Speci Component Iia;
Chain: F, H, G, I, J, P, Q, S, R, T, b, d, c, Z, a, j, k, m
Fragment: Phosphotransferase System, Mannosefructose-Speci Component Iia;
Engineered: Yes
Mutation: Yes

Organism_scientific: Caldanaerobacter Subterraneus Subsp. Tengcongensis (Strain Dsm 15242 Jcm 11007 Nbrc 100824
Organism_taxid: 273068
Strain: Dsm 15242 Jcm 11007 Nbrc 100824 Mb4
Gene: Manx, Tte0192
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: H 3
R_factor 0.227 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
258.820 258.820 641.730 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
ligand
enzyme Transferase E.C.2.5.1.78 BRENDA
Gene MEU
Gene
Ontology
ChainFunctionProcessComponent
H, I, G, F


N, K, B, D, M, C, L, A


S, T, Z, J, Q, P, R


Y, E, W, U, V, O, X


a, d, j, k, c, b, n, m, l


Primary referenceAccurate design of megadalton-scale two-component icosahedral protein complexes., Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D, Science. 2016 Jul 22;353(6297):389-94. doi: 10.1126/science.aaf8818. PMID:27463675
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1761 Kb) [Save to disk]
  • Biological Unit Coordinates (5im4.pdb1.gz) 5211 Kb
  • CSU: Contacts of Structural Units for 5IM4
  • Structure Factors (3360 Kb)
  • Retrieve 5IM4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IM4 from S2C, [Save to disk]
  • Re-refined 5im4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IM4 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 5IM4
  • 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 5im4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5im4] [5im4_b] [5im4_T] [5im4_V] [5im4_L] [5im4_a] [5im4_O] [5im4_G] [5im4_Y] [5im4_R] [5im4_f] [5im4_c] [5im4_j] [5im4_D] [5im4_F] [5im4_h] [5im4_I] [5im4_k] [5im4_W] [5im4_l] [5im4_M] [5im4_n] [5im4_K] [5im4_Q] [5im4_Z] [5im4_S] [5im4_U] [5im4_H] [5im4_i] [5im4_C] [5im4_B] [5im4_N] [5im4_E] [5im4_A] [5im4_J] [5im4_P] [5im4_m] [5im4_d] [5im4_e] [5im4_g] [5im4_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5IM4
  • Community annotation for 5IM4 at PDBWiki (http://pdbwiki.org)

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