3K0B Structural Genomics, Unknown Function date Sep 24, 2009
title Crystal Structure Of A Predicted N6-Adenine-Specific Dna Met From Listeria Monocytogenes Str. 4b F2365
authors B.Nocek, X.Xu, H.Cui, A.Savchenko, A.Edwards, A.Joachimiak, Midwes For Structural Genomics (Mcsg)
compound source
Molecule: Predicted N6-Adenine-Specific Dna Methylase
Chain: A
Engineered: Yes
Organism_scientific: Listeria Monocytogenes Str. 4b
Organism_taxid: 265669
Strain: F2365
Gene: Lmof2365_1916
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21magic
symmetry Space Group: C 1 2 1
R_factor 0.164 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.949 46.156 91.376 90.00 131.09 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand EDO, GOL, MSE enzyme
note 3K0B is a representative structure
Gene LMOF2365
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (3k0b.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 3K0B
  • CSU: Contacts of Structural Units for 3K0B
  • Structure Factors (842 Kb)
  • Retrieve 3K0B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K0B from S2C, [Save to disk]
  • Re-refined 3k0b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K0B 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 3K0B
  • 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 3K0B, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k0b_A] [3k0b]
  • SWISS-PROT database: [Q71YC9]
  • Domain organization of [Q71YC9_LISMF] by SWISSPFAM
  • Domain found in 3K0B: [THUMP ] by SMART
  • Other resources with information on 3K0B
  • Community annotation for 3K0B 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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