3SSE 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(Tgpapgpapcpcpgpgptpapgpc)-
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 0.216 R_Free 0.292
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.046 69.087 143.896 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand
enzyme Hydrolase E.C.3.1.21 BRENDA
Primary referenceThe 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] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (3sse.pdb1.gz) 70 Kb
  • CSU: Contacts of Structural Units for 3SSE
  • Structure Factors (400 Kb)
  • Retrieve 3SSE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SSE from S2C, [Save to disk]
  • Re-refined 3sse structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SSE 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 3SSE
  • 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 3SSE, from MSDmotif at EBI
  • Fold representative 3sse from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sse_B] [3sse_A] [3sse_D] [3sse_C] [3sse]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3SSE
  • Community annotation for 3SSE at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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