1LKM Electron Transport date Apr 25, 2002
title Crystal Structure Of Desulfovibrio Vulgaris Rubrerythrin All Form
authors S.Jin, D.M.Kurtz Jr., Z.J.Liu, J.Rose, B.C.Wang
compound source
Molecule: Rubrerythrin All-Iron(III) Form
Chain: A
Engineered: Yes
 Organism_scientific: Desulfovibrio Vulgaris
Organism_taxid: 881
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: I 2 2 2
R_factor 0.190 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.877 80.609 100.084 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.69 Å
ligand FE enzyme
related structures by homologous chain: 1LKP, 1S2Z
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceX-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase., Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC, J Am Chem Soc 2002 Aug 21;124(33):9845-55. PMID:12175244
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1lkm.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (1lkm.pdb2.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 1LKM
  • CSU: Contacts of Structural Units for 1LKM
  • Likely Quarternary Molecular Structure file(s) for 1LKM
  • Retrieve 1LKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LKM from S2C, [Save to disk]
    • View 1LKM 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 1LKM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1LKM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lkma2, region A:148-191 [Jmol] [rasmolscript] [script source]
        - Domain d1lkma1, region A:2-147 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1lkm] [1lkm_A]
  • SWISS-PROT database: [P24931]
  • Domain organization of [RUBY_DESVH] by SWISSPFAM
    • Other resources with information on 1LKM
  • Community annotation for 1LKM 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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