1MJI	Ribosome	date	Aug 28, 2002
title	Detailed Analysis Of Rna-Protein Interactions Within The Bacterial Ribosomal Protein L55s Rrna Complex
authors	A.Perederina, N.Nevskaya, O.Nikonov, A.Nikulin, P.Dumas, M.Yao, I.Tanaka, M.Garber, G.Gongadze, S.Nikonov
compound		source
Molecule: 5s Rrna Fragment Chain: C, D Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Other_details: In Vitro Transcription
Molecule: 50s Ribosomal Protein L5 Chain: A, B Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
symmetry	Space Group: P 1 21 1	R_factor 0.210 R_Free 0.288
crystal cell	length a length b length c angle alpha angle beta angle gamma 51.890 99.600 65.730 90.00 100.05 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	K, MG, MSE	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex., Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M, Tanaka I, Garber M, Gongadze G, Nikonov S, RNA 2002 Dec;8(12):1548-57. PMID:12515387

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk] Biological Unit Coordinates (1mji.pdb1.gz) 93 Kb LPC: Ligand-Protein Contacts for 1MJI CSU: Contacts of Structural Units for 1MJI Likely Quarternary Molecular Structure file(s) for 1MJI Structure Factors (178 Kb) Retrieve 1MJI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1MJI from S2C, [Save to disk] Re-refined 1mji structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1MJI 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 1MJI

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 3D motif for 1MJI, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1mjia_, region A [Jmol] [rasmolscript] [script source]     - Domain d1mjib_, region B [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1mji_D] [1mji_C] [1mji_A] [1mji_B] [1mji] SWISS-PROT database: [P41201] Domain organization of [RL5_THETH] by SWISSPFAM

Other resources with information on 1MJI

Community annotation for 1MJI at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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Images from IMB Jena Image Library of Biological Macromolecules.

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