5XVP Immune System date Jun 28, 2017
title E. Fae Cas1-Cas2prespacertarget Ternary Complex Revealing Integrated States
authors Y.Xiao, S.Ng, K.H.Nam, A.Ke
compound source
Molecule: Crispr-Associated Endonuclease Cas1
Chain: A, B, C, D
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Enterococcus Faecalis Tx0027
Organism_taxid: 749498
Gene: Cas1, Hmpref9501_02814
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Crispr-Associated Endoribonuclease Cas2
Chain: E, F
Ec: 3.1.-.-
Engineered: Yes

Organism_scientific: Enterococcus Faecalis Tx0027
Organism_taxid: 749498
Gene: Cas2, Hmpref9501_02813
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (73-Mer)
Chain: G
Engineered: Yes
Other_details: Dna

Synthetic: Yes
Organism_scientific: Enterococcus Faecalis Tx0027
Organism_taxid: 749498

Molecule: Dna (73-Mer)
Chain: H
Engineered: Yes
Other_details: Dna

Synthetic: Yes
Organism_scientific: Enterococcus Faecalis Tx0027
Organism_taxid: 749498

Molecule: Dna (5'-D(Ptptpcptpcpcpgpapg)-3')
Chain: I, J
Engineered: Yes
Other_details: Dna

Synthetic: Yes
Organism_scientific: Enterococcus Faecalis Tx0027
Organism_taxid: 749498
symmetry Space Group: I 2 2 2
R_factor 0.194 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.870 212.294 512.199 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand MG enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • nuclease activity
  • endonuclease activity


  • F, E
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity


  • Primary referenceHow type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration., Xiao Y, Ng S, Nam KH, Ke A, Nature. 2017 Sep 4. doi: 10.1038/nature24020. PMID:28869593
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (627 Kb) [Save to disk]
  • Biological Unit Coordinates (5xvp.pdb1.gz) 619 Kb
  • LPC: Ligand-Protein Contacts for 5XVP
  • CSU: Contacts of Structural Units for 5XVP
  • Structure Factors (2187 Kb)
  • Retrieve 5XVP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XVP from S2C, [Save to disk]
  • View 5XVP 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 5XVP
  • 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 5xvp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xvp_I] [5xvp_D] [5xvp_E] [5xvp_F] [5xvp_B] [5xvp_J] [5xvp_C] [5xvp_H] [5xvp_G] [5xvp_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XVP
  • Community annotation for 5XVP at PDBWiki (http://pdbwiki.org)

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