4RTP Transferase Dna date Nov 15, 2014
title Complex Of Escherichia Coli Dna Adenine Methyltransferase (D Adomet 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 0.216 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
35.817 63.225 144.102 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.39 Å
ligand SAM 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 (4rtp.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 4RTP
  • CSU: Contacts of Structural Units for 4RTP
  • Structure Factors (133 Kb)
  • Retrieve 4RTP in mmCIF format [Save to disk]
  • Re-refined 4rtp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RTP 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 4RTP
  • 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 4RTP, from MSDmotif at EBI
  • Fold representative 4rtp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rtp_F] [4rtp_A] [4rtp_G] [4rtp]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4RTP
  • Community annotation for 4RTP at PDBWiki (http://pdbwiki.org)

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