1XEM Hydrolase date Sep 10, 2004
title High Resolution Crystal Structure Of Escherichia Coli Zinc- Deformylase Bound To Formate
authors R.Jain, B.Hao, R.P.Liu, M.K.Chan
compound source
Molecule: Peptide Deformylase
Chain: A
Synonym: Pdf, Polypeptide Deformylase
Ec: 3.5.1.88
Organism_scientific: Escherichia Coli
Organism_taxid: 469008
Strain: Bl21(De3)
symmetry Space Group: P 61 2 2
R_factor 0.163 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.640 54.640 224.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.76 Å
ligand FMT, ZN enzyme Hydrolase E.C.3.5.1.88 BRENDA
related structures by homologous chain: 1G2A, 1XEN
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal., Jain R, Hao B, Liu RP, Chan MK, J Am Chem Soc 2005 Apr 6;127(13):4558-9. PMID:15796505
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (1xem.pdb1.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 1XEM
  • CSU: Contacts of Structural Units for 1XEM
  • Likely Quarternary Molecular Structure file(s) for 1XEM
  • Structure Factors (149 Kb)
  • Retrieve 1XEM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XEM from S2C, [Save to disk]
  • Re-refined 1xem structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XEM 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 1XEM
  • 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 1XEM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xem] [1xem_A]
  • SWISS-PROT database: [P0A6K3]
  • Domain organization of [DEF_ECOLI] by SWISSPFAM
  • Other resources with information on 1XEM
  • Community annotation for 1XEM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science