2VBO Hydrolase date Sep 14, 2007
title Molecular Basis Of Human Xpc Gene Recognition And Cleavage B Engineered Homing Endonuclease Heterodimers
authors P.Redondo, J.Prieto, I.G.Munoz, A.Alibes, F.Stricher, L.Serrano, S C.Perez, J.P.Cabaniols, P.Duchateau, F.Paques, F.J.Blanco, G.Mon
compound source
Molecule: Dna Endonuclease I-Crei
Chain: A
Fragment: Residues 1-153
Synonym: 23s Rrna Intron Protein, Ini3-4-Ca
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Chlamydomonas Reinhardtii
Organism_taxid: 3055
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_variant: D3plyss
Expression_system_plasmid: Cdfduet-1
Other_details: Ini3 Strep-Tag C-Term Ini4 His-Tag C-Term

Molecule: Dna Endonuclease I-Crei
Chain: B
Fragment: Residues 1-153
Synonym: 23s Rrna Intron Protein, Ini3-4-Ca
Ec: 3.1.-.-
Engineered: Yes

Organism_scientific: Chlamydomonas Reinhardtii
Organism_taxid: 3055
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_variant: D3plyss
Expression_system_plasmid: Cdfduet-1
Other_details: Ini3 Strep-Tag C-Term Ini4 His-Tag C-Term

Molecule: 5'-D(Tpcptpgpcpcptptptptp Tptpgpapapgpgpaptpcpcptpapa)-3';
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tptpapgpgpaptpcpcptp Tpcpapapapapapapgpgpcpapgpa)-3';
Chain: E
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.150 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.993 67.950 76.629 90.00 90.10 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CA enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceMolecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases., Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F, Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C, Duchateau P, Paques F, Blanco FJ, Montoya G, Nature. 2008 Nov 6;456(7218):107-11. PMID:18987743
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • Biological Unit Coordinates (2vbo.pdb1.gz) 151 Kb
  • LPC: Ligand-Protein Contacts for 2VBO
  • CSU: Contacts of Structural Units for 2VBO
  • Likely Quarternary Molecular Structure file(s) for 2VBO
  • Structure Factors (581 Kb)
  • Retrieve 2VBO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VBO from S2C, [Save to disk]
  • Re-refined 2vbo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VBO 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 2VBO
  • 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 2VBO, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vbo_B] [2vbo] [2vbo_E] [2vbo_C] [2vbo_A]
  • SWISS-PROT database: [P05725]
  • Domain organization of [DNE1_CHLRE] by SWISSPFAM
  • Other resources with information on 2VBO
  • Community annotation for 2VBO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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