1DFU	Ribosome	date	Nov 21, 1999
title	Crystal Structure Of E.Coli Ribosomal Protein L25 Complexed Rrna Fragment At 1.8 A Resolution
authors	M.Lu, T.A.Steitz
compound		source
Molecule: 5s Rrna Chain: M Fragment: Loop E-Helix Iv Fragment Engineered: Yes Other_details: A Fragment Of 5s Rrna In 50s Ribosomal Subun		Synthetic: Yes Other_details: This Sequence Occurs Naturally In E.Coli
Molecule: 5s Rrna Chain: N Fragment: Loop E-Helix Iv Fragment Engineered: Yes Other_details: A Fragment Of 5s Rrna In 50s Ribosomal Subun		Synthetic: Yes Other_details: This Sequence Occurs Naturally In E.Coli
Molecule: Ribosomal Protein L25 Chain: P Engineered: Yes Other_details: Protein From The Large Ribosomal Subunit		Organism_scientific: Escherichia Coli Organism_taxid: 562 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pl25
symmetry	Space Group: C 2 2 21	R_factor 0.207 R_Free 0.225
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.600 76.600 95.100 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	MG	enzyme
related structures	by homologous chain: 1D6K
Gene Ontology	Chain Function Process Component P
Primary reference	Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution., Lu M, Steitz TA, Proc Natl Acad Sci U S A 2000 Feb 29;97(5):2023-8. PMID:10696113

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk] Biological Unit Coordinates (1dfu.pdb1.gz) 37 Kb LPC: Ligand-Protein Contacts for 1DFU CSU: Contacts of Structural Units for 1DFU Likely Quarternary Molecular Structure file(s) for 1DFU Structure Factors (210 Kb) Retrieve 1DFU in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DFU from S2C, [Save to disk] Re-refined 1dfu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1DFU 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 1DFU

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 1DFU, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dfup_, region P [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: [1dfu_N] [1dfu_M] [1dfu] [1dfu_P] SWISS-PROT database: [P68919] Domain organization of [RL25_ECOLI] by SWISSPFAM

Other resources with information on 1DFU

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

Movements, Movies and Images

Domain movements in 1DFU from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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