5D8H	Ribosomal Protein	date	Aug 17, 2015
title	Crystal Structure Of The Base Of The Ribosomal P Stalk From Methanococcus Jannaschii With Antibiotic Thiostrepton
authors	A.G.Gabdulkhakov, I.V.Mitroshin, M.B.Garber
compound		source
Molecule: 23s Ribosomal Rna Chain: A Engineered: Yes		Organism_scientific: Methanocaldococcus Jannaschii Organism_taxid: 2190 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Xl1(Blue) Expression_system_vector_type: Puc18 Expression_system_plasmid: Pmja23s-74.Uc18
Molecule: 50s Ribosomal Protein L10 Chain: B Fragment: Unp Residues 9-221 Synonym: Acidic Ribosomal Protein P0 Homolog,Mjal10 Engineered: Yes Mutation: Yes		Organism_scientific: Methanocaldococcus Jannaschii Organism_taxid: 2190 Gene: Rpl10, Rplp0, Mj0509 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_variant: Pubs520 Expression_system_vector_type: Plasmid Expression_system_vector: Pet-11c Expression_system_plasmid: Pet-11cmjap0ntf
Molecule: 50s Ribosomal Protein L11 Chain: C Engineered: Yes		Organism_scientific: Methanocaldococcus Jannaschii Organism_taxid: 2190 Gene: Rpl11, Mj0373 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_variant: Pubs520 Expression_system_vector_type: Pet-11c Expression_system_plasmid: Pet-11cmjal11
Molecule: Thiostrepton Chain: D		Organism_scientific: Streptomyces Azureus Organism_taxid: 146537
symmetry	Space Group: I 2 2 2	R_factor 0.208 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 125.070 127.160 132.930 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	BB9, DBU, DCY, DHA, MG, MH6, MSE, NA, NH2, QUA, TRS, TS9	enzyme
Gene Ontology	Chain Function Process Component B C

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk] Biological Unit Coordinates (5d8h.pdb1.gz) 95 Kb LPC: Ligand-Protein Contacts for 5D8H CSU: Contacts of Structural Units for 5D8H Structure Factors (407 Kb) Retrieve 5D8H in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D8H from S2C, [Save to disk] Re-refined 5d8h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D8H 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 5D8H

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5d8h_B] [5d8h_A] [5d8h_C] [5d8h] [5d8h_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5D8H: [RL11 ] by SMART

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