5FFJ Dna Binding Protein Dna date Dec 18, 2015
title Structure Of A Nuclease-Deletion Mutant Of The Type Isp Rest Modification Enzyme Llagi In Complex With A Dna Substrate M
authors K.Saikrishnan, M.Kulkarni, N.Nirwan
compound source
Molecule: Endonuclease And Methylase Llagi
Chain: A, B
Fragment: Unp Residues 166-1570
Engineered: Yes
 Organism_scientific: Lactococcus Lactis
Organism_taxid: 1358
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Ptpcpcptpcpcpaptpcpcpapgptpcptpaptptpa -3');
Chain: D, E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Dna (5'- D(Ptpapgpcptpapaptpapgpapcptpgpgpaptpgpg -3');
Chain: C, F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.400 222.290 117.410 90.00 105.14 90.00
method X-Ray Diffractionresolution 2.84 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural insights into DNA sequence recognition by Type ISP restriction-modification enzymes., Kulkarni M, Nirwan N, van Aelst K, Szczelkun MD, Saikrishnan K, Nucleic Acids Res. 2016 Mar 14. pii: gkw154. PMID:26975655
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (712 Kb) [Save to disk]
  • Biological Unit Coordinates (5ffj.pdb1.gz) 329 Kb
  • Biological Unit Coordinates (5ffj.pdb2.gz) 379 Kb
  • CSU: Contacts of Structural Units for 5FFJ
  • Structure Factors (1996 Kb)
  • Retrieve 5FFJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FFJ from S2C, [Save to disk]
  • Re-refined 5ffj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5FFJ 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 5FFJ
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ffj_E] [5ffj_D] [5ffj] [5ffj_A] [5ffj_B] [5ffj_F] [5ffj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5FFJ: [DEXDc] [HELICc ] by SMART
    • Other resources with information on 5FFJ
  • Community annotation for 5FFJ at PDBWiki (http://pdbwiki.org)

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