5EF1 Rna Binding Protein date Oct 23, 2015
title Radiation Damage To The Trap-Rna Complex: Dose (Dwd) 19.3 Mg
authors C.S.Bury, J.E.Mcgeehan, E.F.Garman, M.B.Shevtsov
compound source
Molecule: Transcription Attenuation Protein Mtrb
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R V;
Synonym: Trp Rna-Binding Attenuation Protein,Trap,Tryptopha Binding Attenuator Protein;
Engineered: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Mtrb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Sg62052pgp1-2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptzstmtrb

Molecule: (Gaguu)10gag 53-Nucleotide Rna
Chain: W
Fragment: (Gaguu)10gag 53-Nucleotide Rna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Rna. In-Vitro Transcription
symmetry Space Group: C 1 2 1
R_factor 0.230 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
141.190 111.170 138.210 90.00 117.39 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand TRP enzyme
Gene
Ontology
ChainFunctionProcessComponent
S, F, T, N, K, E, V, Q, M, C, L, A, J, O, P, B, H, D, R, I, G, U


Primary referenceRNA protects a nucleoprotein complex against radiation damage., Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF, Acta Crystallogr D Struct Biol. 2016 May 1;72(Pt 5):648-57. doi:, 10.1107/S2059798316003351. Epub 2016 Apr 26. PMID:27139628
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (287 Kb) [Save to disk]
  • Biological Unit Coordinates (5ef1.pdb1.gz) 131 Kb
  • Biological Unit Coordinates (5ef1.pdb2.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 5EF1
  • CSU: Contacts of Structural Units for 5EF1
  • Structure Factors (8713 Kb)
  • Retrieve 5EF1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EF1 from S2C, [Save to disk]
  • Re-refined 5ef1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EF1 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 5EF1
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1w5ef1, region F:23-231 [Jmol] [rasmolscript] [script source]
  • Fold representative 5ef1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ef1_T] [5ef1_D] [5ef1_N] [5ef1_S] [5ef1_B] [5ef1_U] [5ef1_P] [5ef1] [5ef1_H] [5ef1_W] [5ef1_A] [5ef1_J] [5ef1_F] [5ef1_R] [5ef1_M] [5ef1_I] [5ef1_L] [5ef1_V] [5ef1_E] [5ef1_C] [5ef1_Q] [5ef1_K] [5ef1_G] [5ef1_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EF1
  • Community annotation for 5EF1 at PDBWiki (http://pdbwiki.org)

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