6GCD Dna Binding Protein date Apr 17, 2018
title Dna Binding Domain Of Restriction Endonuclease Mcrbc In Comp 5-Hydroxymethylcytosine Dna
authors G.Sasnauskas, E.Manakova
compound source
Molecule: 5-Methylcytosine-Specific Restriction Enzyme B
Chain: A, B
Synonym: Ecokmcrbc
Ec: 3.1.21.-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Mcrb, Rglb, B4346, Jw5871
Expression_system: Escherichia Coli Str. K-12 Substr. Dh10b
Expression_system_taxid: 316385

Molecule: Dna (5'-D(Gpapgpap(5hc)Pcpgpgptpapgpc
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpap(5hc)Pcpgpgptpcptpc
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.166 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.071 68.934 143.708 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 5HC, CME enzyme Hydrolase E.C.3.1.21 BRENDA
Primary referenceRecognition of modified cytosine variants by the DNA binding domain of methyl-directed endonuclease McrBC., Zagorskaite E, Manakova E, Sasnauskas G, FEBS Lett. 2018 Sep 8. doi: 10.1002/1873-3468.13244. PMID:30194838
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (6gcd.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 6GCD
  • CSU: Contacts of Structural Units for 6GCD
  • Structure Factors (1007 Kb)
  • Retrieve 6GCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6GCD from S2C, [Save to disk]
  • View 6GCD 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 6GCD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6gcd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6gcd_B] [6gcd_A] [6gcd_D] [6gcd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6GCD
  • Community annotation for 6GCD at PDBWiki (http://pdbwiki.org)

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