1X6J Structural Genomics, Unknown Function date Aug 11, 2004
title Crystal Structure Of Ygfy From Escherichia Coli
authors K.Lim, V.Doseeva, E.Sarikaya Demirkan, S.Pullalarevu, W.Krajewsk A.Galkin, A.Howard, O.Herzberg, Structure 2 Function Project (
compound source
Molecule: Hypothetical Protein Ygfy
Chain: A
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Ygfy
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Star (De3)
Expression_system_vector_type: Pet100d-Topo
symmetry Space Group: I 2 2 2
R_factor 0.188 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.400 42.700 84.900 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
related structures by homologous chain: 1X6I
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the YgfY from Escherichia coli, a protein that may be involved in transcriptional regulation., Lim K, Doseeva V, Demirkan ES, Pullalarevu S, Krajewski W, Galkin A, Howard A, Herzberg O, Proteins 2004 Dec 8;58(3):759-763. PMID:15593094
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (19 Kb) [Save to disk]
  • Biological Unit Coordinates (1x6j.pdb1.gz) 16 Kb
  • CSU: Contacts of Structural Units for 1X6J
  • Likely Quarternary Molecular Structure file(s) for 1X6J
  • Structure Factors (47 Kb)
  • Retrieve 1X6J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1X6J from S2C, [Save to disk]
  • Re-refined 1x6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1X6J 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 1X6J
  • 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 1X6J, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1x6j] [1x6j_A]
  • SWISS-PROT database: [P64559]
  • Domain organization of [YGFY_ECOLI] by SWISSPFAM
    • Other resources with information on 1X6J
  • Community annotation for 1X6J 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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