4RTN Transferase Dna date Nov 15, 2014
title Complex Of Escherichia Coli Dna Adenine Methyltransferase (D Adohcy And With Dna Containing Proximal Pap Regulon Sequenc
authors J.R.Horton, X.Cheng
compound source
Molecule: Dna Adenine Methylase
Chain: A
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 1110693
Strain: K-12 Substr. Mds42
Gene: Dam, Ecmds42_2833
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Hms174(De3)
Expression_system_vector_type: Plasmid

Molecule: Dna (5'-D(Tptptpapapapgpaptpcpg)-3')
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Apcpgpaptpcptptptpapa)-3')
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.201 63.477 144.048 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.59 Å
ligand SAH enzyme
Gene ECMDS42
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression., Horton JR, Zhang X, Blumenthal RM, Cheng X, Nucleic Acids Res. 2015 Apr 6. pii: gkv251. PMID:25845600
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (4rtn.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 4RTN
  • CSU: Contacts of Structural Units for 4RTN
  • Structure Factors (98 Kb)
  • Retrieve 4RTN in mmCIF format [Save to disk]
  • Re-refined 4rtn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RTN 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 4RTN
  • 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 4RTN, from MSDmotif at EBI
  • Fold representative 4rtn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rtn_A] [4rtn] [4rtn_G] [4rtn_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4RTN
  • Community annotation for 4RTN at PDBWiki (http://pdbwiki.org)

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