4AQU Hydrolase date Apr 19, 2012
title Crystal Structure Of I-Crei Complexed With Its Target Methyl Position Plus 2 (In The B Strand) In The Presence Of Calciu
authors J.Valton, F.Daboussi, S.Leduc, P.Redondo, R.Macmaster, R.Molina, G P.Duchateau
compound source
Molecule: Dna Endonuclease I-Crei
Chain: A, B
Fragment: Residues 2-153
Synonym: 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_vector_type: Plasmid
Expression_system_vector: Pet24d
Expression_system_plasmid: Cdfduet1

Molecule: 5'-D(Dtpcpapapapapcpgptpcpgptpgpdap Gpapcpapgptptptpgpg)-3';
Chain: C

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Dcpcpapapapcptpgptpcptpcpap5cm Gpapcpgptptptptpgpa)-3';
Chain: D

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 2 21
R_factor 0.1959 R_Free 0.2487
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.580 45.355 172.331 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 5CM, CA, GOL enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary reference5'-Cytosine-phosphoguanine (CpG) methylation impacts the activity of natural and engineered meganucleases., Valton J, Daboussi F, Leduc S, Molina R, Redondo P, Macmaster R, Montoya G, Duchateau P, J Biol Chem. 2012 Aug 31;287(36):30139-50. Epub 2012 Jun 27. PMID:22740697
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (4aqu.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 4AQU
  • CSU: Contacts of Structural Units for 4AQU
  • Structure Factors (552 Kb)
  • Retrieve 4AQU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AQU from S2C, [Save to disk]
  • Re-refined 4aqu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AQU 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 4AQU
  • 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 4AQU, from MSDmotif at EBI
  • Fold representative 4aqu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4aqu_B] [4aqu_D] [4aqu] [4aqu_C] [4aqu_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4AQU
  • Community annotation for 4AQU at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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