2VBL 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: Amel3-4-Mg, 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 1-153
Synonym: Amel3-4-Mg, 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(Dtdcdtdgdcdcdtdtdtdtdtdt Dgpdap)-3';
Chain: C

Synthetic: Yes

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

Synthetic: Yes

Molecule: 5'-D(Dtdtdadgdgdadtdcdcdtdtdc Dapdap)-3';
Chain: E

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.147 R_Free 0.197
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.612 69.209 88.671 90.00 95.46 90.00
method X-Ray Diffractionresolution 1.8 Å
ligand 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] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (2vbl.pdb1.gz) 157 Kb
  • LPC: Ligand-Protein Contacts for 2VBL
  • CSU: Contacts of Structural Units for 2VBL
  • Likely Quarternary Molecular Structure file(s) for 2VBL
  • Structure Factors (635 Kb)
  • Retrieve 2VBL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VBL from S2C, [Save to disk]
  • Re-refined 2vbl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VBL 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 2VBL
  • 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 2VBL, from MSDmotif at EBI
  • Fold representative 2vbl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vbl_A] [2vbl_C] [2vbl_S] [2vbl_E] [2vbl_T] [2vbl_B] [2vbl]
  • SWISS-PROT database: [P05725]
  • Domain organization of [DNE1_CHLRE] by SWISSPFAM
  • Other resources with information on 2VBL
  • Community annotation for 2VBL 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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