1Y0V Lyase date Nov 16, 2004
title Crystal Structure Of Anthrax Edema Factor (Ef) In Complex With Calmodulin And Pyrophosphate
authors Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florian, W.J.Tang
compound source
Molecule: Calmodulin-Sensitive Adenylate Cyclase
Chain: A, B, C, D, E, F
Synonym: Atp Pyrophosphate-Lyase, Adenylyl Cyclase, Edema Factor, Ef, Anthrax Edema Toxin Adenylate Cyclase Component;
Ec: 4.6.1.1
Engineered: Yes
 Organism_scientific: Bacillus Anthracis
Organism_taxid: 1392
Gene: Cya
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid

Molecule: Calmodulin
Chain: H, I, J, K, L, M
Synonym: Cam
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Calm1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
symmetry Space Group: C 1 2 1
R_factor 0.286 R_Free 0.307
crystal
cell
length a length b length c angle alpha angle beta angle gamma
317.509 183.348 141.812 90.00 90.05 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand CA, MG, POP enzyme Lyase E.C.4.6.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, C, D
  • nucleotide binding
  • adenylate cyclase activity
  • protein binding
  • calmodulin binding
  • ATP binding
  • lyase activity
  • metal ion binding
  • cAMP biosynthetic process
  • pathogenesis
  • extracellular region
    • J, K, H, M, I, L
  • receptor binding
  • calcium ion binding
  • protein binding
  • metal ion binding


    • Primary referenceCalcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor., Shen Y, Zhukovskaya NL, Guo Q, Florian J, Tang WJ, EMBO J 2005 Mar 9;24(5):929-41. Epub 2005 Feb 17. PMID:15719022
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (887 Kb) [Save to disk]
  • Biological Unit Coordinates (1y0v.pdb1.gz) 153 Kb
  • Biological Unit Coordinates (1y0v.pdb2.gz) 153 Kb
  • Biological Unit Coordinates (1y0v.pdb3.gz) 153 Kb
  • Biological Unit Coordinates (1y0v.pdb4.gz) 152 Kb
  • Biological Unit Coordinates (1y0v.pdb5.gz) 153 Kb
  • Biological Unit Coordinates (1y0v.pdb6.gz) 153 Kb
  • LPC: Ligand-Protein Contacts for 1Y0V
  • CSU: Contacts of Structural Units for 1Y0V
  • Likely Quarternary Molecular Structure file(s) for 1Y0V
  • Retrieve 1Y0V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y0V from S2C, [Save to disk]
    • View 1Y0V 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1Y0V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1Y0V, from MSDmotif at EBI
  • Fold representative 1y0v from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y0v_A] [1y0v_B] [1y0v_C] [1y0v_D] [1y0v_E] [1y0v_F] [1y0v_H] [1y0v_I] [1y0v_J] [1y0v_K] [1y0v_L] [1y0v_M]
  • SWISS-PROT database: [P62155] [P40136]
  • Domain organization of [CALM_XENLA] [CYAA_BACAN] by SWISSPFAM
  • Domain found in 1Y0V: [EFh ] by SMART
  • Alignments of the sequence of 1Y0V with the sequences similar proteins can be viewed for 1Y0V's classification [CALM_XENLA] [CYAA_BACAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CALM_XENLA] [CYAA_BACAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1Y0V
  • Community annotation for 1Y0V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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