6XNZ Recombination date Jul 05, 2020
title Structure Of Rag1 (R848me649v)-Rag2-Dna Target Capture Comp
authors Y.Zhang, E.Corbett, S.Wu, D.G.Schatz
compound source
Molecule: V(D)J Recombination-Activating Protein 1
Chain: A, C
Synonym: Rag-1
Ec: 3.1.-.-,2.3.2.27
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: V(D)J Recombination-Activating Protein 2
Chain: B, D
Synonym: Rag-2
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag2, Rag-2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: Target Dna Top Strand (37-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: Target Dna Bottom Strand (37-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: 12rss Integration Strand (34-Mer)
Chain: x
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: 12rss Non-Integration Strand (34-Mer)
Chain: M
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: 23rss Integration Strand (45-Mer)
Chain: y
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: 23rss Non-Integration Strand (45-Mer)
Chain: L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
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 Microscopyresolution 3.80 Å
ligand ZN enzyme Hydrolase E.C.3.1 BRENDA
Primary referenceStructural basis for the activation and suppression of transposition during evolution of the RAG recombinase., Zhang Y, Corbett E, Wu S, Schatz DG, EMBO J. 2020 Sep 18:e105857. doi: 10.15252/embj.2020105857. PMID:32945578
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (303 Kb) [Save to disk]
  • Biological Unit Coordinates (6xnz.pdb1.gz) 290 Kb
  • LPC: Ligand-Protein Contacts for 6XNZ
  • CSU: Contacts of Structural Units for 6XNZ
  • Retrieve 6XNZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6XNZ from S2C, [Save to disk]
  • View 6XNZ 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 6XNZ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6xnz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6xnz_B] [6xnz_C] [6xnz_D] [6xnz_J] [6xnz_A] [6xnz_M] [6xnz_x] [6xnz_I] [6xnz_y] [6xnz_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6XNZ
  • Community annotation for 6XNZ at PDBWiki (http://pdbwiki.org)

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