3CKM Biosynthetic Protein date Mar 16, 2008
title Lpoa (Yram) C-Domain From Haemophilus Influenzae, A Regulato
authors J.Vijayalakshmi, M.A.Saper
compound source
Molecule: Yram (Hi1655)
Chain: A
Fragment: C-Terminal Domain, Unp Residues 256-573
Synonym: Lpoa
Engineered: Yes
 Organism_scientific: Haemophilus Influenzae
Organism_taxid: 71421
Strain: Rd Kw20
Gene: Yram
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami (De3) Placi
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petblue-2
symmetry Space Group: C 1 2 1
R_factor 0.157 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.907 50.644 63.676 90.00 106.73 90.00
method X-Ray Diffractionresolution 1.35 Å
ligand BME, MSE, SO4 enzyme
note 3CKM is a representative structure and supersedes 2H4A
Primary referenceStructure of YraM, a protein essential for growth of Haemophilus influenzae., Vijayalakshmi J, Akerley BJ, Saper MA, Proteins. 2008 Apr 15;. PMID:18412262
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (3ckm.pdb1.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 3CKM
  • CSU: Contacts of Structural Units for 3CKM
  • Likely Quarternary Molecular Structure file(s) for 3CKM
  • Structure Factors (9953 Kb)
  • Retrieve 3CKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CKM from S2C, [Save to disk]
  • Re-refined 3ckm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3CKM 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 3CKM
  • 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 3CKM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ckm] [3ckm_A]
  • SWISS-PROT database: [P45299]
  • Domain organization of [Y1655_HAEIN] by SWISSPFAM
    • Other resources with information on 3CKM
  • Community annotation for 3CKM 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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