487D	Ribosome	date	Feb 23, 2000
title	Seven Ribosomal Proteins Fitted To A Cryo-Electron Microscop The Large 50s Subunit At 7.5 Angstroms Resolution
authors	R.Brimacombe, F.Mueller
compound		source
Molecule: 50s Ribosomal Protein L1 Chain: H		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 50s Ribosomal Protein L2 Chain: I Synonym: Bstl2,L3		Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422
Molecule: 50s Ribosomal Protein L6 Chain: J Synonym: Bl10		Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422
Molecule: 50s Ribosomal Protein L9 Chain: K Synonym: Bl17		Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422
Molecule: 50s Ribosomal Protein L11 Chain: L		Organism_scientific: Thermotoga Maritima Organism_taxid: 2336
Molecule: 50s Ribosomal Protein L14 Chain: M		Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422
Molecule: 50s Ribosomal Protein L25 Chain: N		Organism_scientific: Escherichia Coli Organism_taxid: 562
symmetry	Space Group: P 1	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 1.000 1.000 1.000 90.00 90.00 90.00
method	Electron Microscopy	resolution	7.50 Å
ligand	FMT, MSE, NH2	enzyme
Gene Ontology	Chain Function Process Component H I J K L M N
Primary reference	The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution., Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, Wohnert J, Gorlach M, van Heel M, Brimacombe R, J Mol Biol 2000 Apr 21;298(1):35-59. PMID:10756104

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (176 Kb) [Save to disk] Biological Unit Coordinates (487d.pdb1.gz) 174 Kb LPC: Ligand-Protein Contacts for 487D CSU: Contacts of Structural Units for 487D Likely Quarternary Molecular Structure file(s) for 487D Retrieve 487D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 487D from S2C, [Save to disk]

View 487D 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 487D

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 487D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d487dh_, region H [Jmol] [rasmolscript] [script source]     - Domain d487di_, region I [Jmol] [rasmolscript] [script source]     - Domain d487dj_, region J [Jmol] [rasmolscript] [script source]     - Domain d487dk_, region K [Jmol] [rasmolscript] [script source]     - Domain d487dl_, region L [Jmol] [rasmolscript] [script source]     - Domain d487dm_, region M [Jmol] [rasmolscript] [script source]     - Domain d487dn_, region N [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [487d_M] [487d_H] [487d_J] [487d] [487d_I] [487d_N] [487d_L] [487d_K] SWISS-PROT database: [P0A7J7] [P0A7L0] [P68919] [P60422] [P0A7R1] Domain organization of [RL11_ECOLI] [RL1_ECOLI] [RL25_ECOLI] [RL2_ECOLI] [RL9_ECOLI] by SWISSPFAM Domains found in 487D: [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART

Other resources with information on 487D

Community annotation for 487D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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