3GNA	Recombination	date	Mar 16, 2009
title	Crystal Structure Of The Rag1 Nonamer-Binding Domain With Dn
authors	F.F.Yin, S.Bailey, C.A.Innis, T.A.Steitz, D.G.Schatz
compound		source
Molecule: V(D)J Recombination-Activating Protein 1 Chain: A Fragment: Nonamer Binding Domain: Unp Residues 389-456 Synonym: Rag-1 Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Gene: Rag1, Rag-1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: 5'-D(Apcptptpapapcpapapapapapcpc)-3 Chain: D Engineered: Yes		Synthetic: Yes Other_details: Synthetic Dna
Molecule: 5'-D(Tpgpgptptptptptpgptptpapapg)-3 Chain: E Engineered: Yes		Synthetic: Yes Other_details: Synthetic Dna
symmetry	Space Group: I 4 2 2	R_factor 0.236 R_Free 0.271
crystal cell	length a length b length c angle alpha angle beta angle gamma 97.470 97.470 69.780 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
Gene Ontology	Chain Function Process Component A
Primary reference	Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis., Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG, Nat Struct Mol Biol. 2009 May;16(5):499-508. Epub 2009 Apr 26. PMID:19396172

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk] Biological Unit Coordinates (3gna.pdb1.gz) 43 Kb CSU: Contacts of Structural Units for 3GNA Likely Quarternary Molecular Structure file(s) for 3GNA Structure Factors (49 Kb) Retrieve 3GNA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GNA from S2C, [Save to disk] Re-refined 3gna structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GNA 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 3GNA

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 3GNA, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gna_E] [3gna_A] [3gna_D] [3gna] SWISS-PROT database: [P15919] Domain organization of [RAG1_MOUSE] by SWISSPFAM

Other resources with information on 3GNA

Community annotation for 3GNA at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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