2VBJ Hydrolase Dna 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 2-153
Synonym: Amel3-4-Ca, 23s Rrna Intron Protein
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: Amel4 Strep-Tag C-Term Amel3 His-Tag C-Term

Molecule: Dna Endonuclease I-Crei
Chain: B
Fragment: Residues 2-153
Synonym: Amel3-4-Ca, 23s Rrna Intron Protein
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: Amel4 Strep-Tag C-Term Amel3 His-Tag C-Term

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.147 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.552 68.700 88.731 90.00 95.36 90.00
method X-Ray Diffractionresolution 1.95 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] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (2vbj.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 2VBJ
  • CSU: Contacts of Structural Units for 2VBJ
  • Likely Quarternary Molecular Structure file(s) for 2VBJ
  • Structure Factors (499 Kb)
  • Retrieve 2VBJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VBJ from S2C, [Save to disk]
  • Re-refined 2vbj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VBJ 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 2VBJ
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VBJ, from MSDmotif at EBI
  • Fold representative 2vbj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vbj_B] [2vbj_A] [2vbj] [2vbj_C] [2vbj_E]
  • SWISS-PROT database: [P05725]
  • Domain organization of [DNE1_CHLRE] by SWISSPFAM
  • Other resources with information on 2VBJ
  • Community annotation for 2VBJ 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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