5BR8 Ribosome date May 29, 2015
title Ambient-Temperature Crystal Structure Of 30s Ribosomal Subun Thermus Thermophilus In Complex With Paromomycin
authors R.G.Sierra, C.Gati, H.Laksmono, E.H.Dao, S.Gul, F.Fuller, J.Kern, R.Chatterjee, M.Ibrahim, A.Brewster, I.D.Young, T.Michels-Clark A.Aquila, L.Mengning, M.S.Hunter, J.E.Koglin, S.Boutet, E.A.Junc B.Hayes, M.J.Bogan, C.Y.Hampton, E.V.Puglisi, N.K.Sauter, C.A.St A.Zouni, J.Yano, V.K.Yachandra, S.M.Soltis, J.D.Puglisi, H.Demir
compound source
Molecule: 16s Ribosomal Rna
Chain: A
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S2
Chain: B

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S3
Chain: C

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S4
Chain: D

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S5
Chain: E

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S7
Chain: G

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S8
Chain: H

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S9
Chain: I

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S10
Chain: J

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S11
Chain: K

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S12
Chain: L

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S13
Chain: M

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S15
Chain: O

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S16
Chain: P

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S17
Chain: Q

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S18
Chain: R

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S19
Chain: S

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein S20
Chain: T

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: 30s Ribosomal Protein Thx
Chain: U
Synonym: S31

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
symmetry Space Group: P 41 21 2
R_factor 0.193 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.300 401.300 176.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand 0TD, 2MG, 4OC, 5MC, G7M, M2G, MA6, MG, PAR, PSU, UR3, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2272 Kb) [Save to disk]
  • Biological Unit Coordinates (5br8.pdb1.gz) 2229 Kb
  • LPC: Ligand-Protein Contacts for 5BR8
  • CSU: Contacts of Structural Units for 5BR8
  • Structure Factors (2916 Kb)
  • Retrieve 5BR8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BR8 from S2C, [Save to disk]
  • Re-refined 5br8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BR8 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 5BR8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5br8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5br8_E] [5br8_S] [5br8_J] [5br8_K] [5br8_N] [5br8_T] [5br8_Q] [5br8_P] [5br8_C] [5br8_A] [5br8_F] [5br8_M] [5br8_G] [5br8] [5br8_B] [5br8_H] [5br8_L] [5br8_R] [5br8_D] [5br8_I] [5br8_U] [5br8_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5BR8: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 5BR8
  • Community annotation for 5BR8 at PDBWiki (http://pdbwiki.org)

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