2VBN Hydrolase date Sep 14, 2007
title Molecular Basis Of Human Xpc Gene Recognition And Cleavage By Engineered Homing Endonuclease Heterodimers
authors P.Redondo, J.Prieto, I.G.Munoz, A.Alibes, F.Stricher, L.Serrano, S.Arnould, C.Perez, J.P.Cabaniols, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya
compound source
Molecule: Dna Endonuclease I-Crei
Chain: A
Fragment: Residues 1-153
Synonym: 23s Rrna Intron Protein, Ini3-4-Mg
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-Mg
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(Tptpapgpgpaptpcpcptp Tpcpapap)-3';
Chain: C

Synthetic: Yes

Molecule: 5'-D(Apapapapgpgpcpapgpap)-3'
Chain: S

Synthetic: Yes

Molecule: 5'-D(Tpcptpgpcpcptptptptp Tptpgpap)-3';
Chain: E

Synthetic: Yes

Molecule: 5'-D(Apgpgpaptpcpcptpapap)-3'
Chain: T

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.141 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.115 67.992 77.186 90.00 90.11 90.00
method X-Ray Diffractionresolution 1.9 Å
ligand CA, MG 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] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (2vbn.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 2VBN
  • CSU: Contacts of Structural Units for 2VBN
  • Likely Quarternary Molecular Structure file(s) for 2VBN
  • Structure Factors (478 Kb)
  • Retrieve 2VBN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VBN from S2C, [Save to disk]
  • Re-refined 2vbn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VBN 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 2VBN
  • 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 2VBN, from MSDmotif at EBI
  • Fold representative 2vbn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vbn_T] [2vbn_B] [2vbn_C] [2vbn_A] [2vbn_E] [2vbn] [2vbn_S]
  • SWISS-PROT database: [P05725]
  • Domain organization of [DNE1_CHLRE] by SWISSPFAM
  • Other resources with information on 2VBN
  • Community annotation for 2VBN 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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