3SSD	Dna Binding Protein Dna	date	Jul 08, 2011
title	Dna Binding Domain Of Restriction Endonuclease Bound To Dna
authors	R.Sukackaite, S.Grazulis, V.Siksnys
compound		source
Molecule: 5-Methylcytosine-Specific Restriction Enzyme B Chain: A, B Fragment: N-Terminal Dna Binding Domain Synonym: Ecokmcrbc Ec: 3.1.21.- Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12 Gene: Mcrb Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Er2267 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pbad24
Molecule: Dna (5'-D(Tgpapgpap(5cm)Pcpgpgptpapgp Chain: C Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Agpcptpapcpcpgpgptpcptpc)- Chain: D Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 21 21 21	R_factor 0.196 R_Free 0.262
crystal cell	length a length b length c angle alpha angle beta angle gamma 36.085 67.189 142.414 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	5CM	enzyme	Hydrolase E.C.3.1.21 BRENDA
Primary reference	The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine., Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V, Nucleic Acids Res. 2012 May 8. PMID:22570415

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk] Biological Unit Coordinates (3ssd.pdb1.gz) 144 Kb LPC: Ligand-Protein Contacts for 3SSD CSU: Contacts of Structural Units for 3SSD Structure Factors (367 Kb) Retrieve 3SSD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3SSD from S2C, [Save to disk] Re-refined 3ssd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3SSD 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 3SSD

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 3D motif for 3SSD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ssd_A] [3ssd_B] [3ssd_C] [3ssd] [3ssd_D] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3SSD

Community annotation for 3SSD at PDBWiki (http://pdbwiki.org)

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