1YF3 Transferase Dna date Dec 30, 2004
title T4dam In Complex With Adohcy And 13-Mer Oligonucleotide Maki And Semi-Specific (~14) Contact
authors J.R.Horton, K.Liebert, S.Hattman, A.Jeltsch, X.Cheng
compound source
Molecule: 5'-D(Apcpcpaptpgpaptpcptpgpapc)-3'
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: Synthesized By New England Biolabs

Molecule: 5'-D(Tpgptpcpapgpaptpcpaptpgpg)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By New England Biolabs

Molecule: Dna Adenine Methylase
Chain: A, B
Synonym: Deoxyadenosyl-Methyltransferase, M.Ecot4dam
Ec: 2.1.1.72
Engineered: Yes

Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
Gene: Dam
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Gm 2971
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pjw2
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.900 125.800 73.200 90.00 104.70 90.00
method X-Ray Diffractionresolution 2.29 Å
ligand GOL, SAH enzyme Transferase E.C.2.1.1.72 BRENDA
related structures by homologous chain: 1Q0S
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceTransition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase., Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X, Cell 2005 May 6;121(3):349-61. PMID:15882618
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (1yf3.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 1YF3
  • CSU: Contacts of Structural Units for 1YF3
  • Likely Quarternary Molecular Structure file(s) for 1YF3
  • Retrieve 1YF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YF3 from S2C, [Save to disk]
  • View 1YF3 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 1YF3
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1YF3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yf3_D] [1yf3_A] [1yf3_C] [1yf3_B] [1yf3]
  • SWISS-PROT database: [P04392]
  • Domain organization of [DMA_BPT4] by SWISSPFAM
  • Other resources with information on 1YF3
  • Community annotation for 1YF3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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