4JCY Dna Binding Protein Dna date Feb 22, 2013
title Crystal Structure Of The Restriction-Modification Controller C.Csp231i Or Operator Complex
authors M.B.Shevtsov, S.D.Streeter, S.J.Thresh, J.E.Mcgeehan, G.G.Kneale
compound source
Molecule: Csp231i C Protein
Chain: A, B
Engineered: Yes
Organism_scientific: Citrobacter Sp. Rfl231
Organism_taxid: 315237
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-11a

Molecule: Dna (5'- D(Apapapcptpapapgpapapapaptpcptptpapgpcp 3');
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Tptpgpcptpapapgpaptptptptpcptptpapgptp 3');
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 61
R_factor 0.147 R_Free 0.163
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.340 62.340 158.080 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand IOD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression., Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A, McGeehan JE, Kneale GG, Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):398-407. doi:, 10.1107/S139900471402690X. Epub 2015 Jan 23. PMID:25664751
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (4jcy.pdb1.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 4JCY
  • CSU: Contacts of Structural Units for 4JCY
  • Structure Factors (452 Kb)
  • Retrieve 4JCY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JCY from S2C, [Save to disk]
  • Re-refined 4jcy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JCY 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 4JCY
  • 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 4JCY, from MSDmotif at EBI
  • Fold representative 4jcy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jcy] [4jcy_B] [4jcy_A] [4jcy_C] [4jcy_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4JCY: [HTH_XRE ] by SMART
  • Other resources with information on 4JCY
  • Community annotation for 4JCY at PDBWiki (http://pdbwiki.org)

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