2X5A Viral Protein date Feb 07, 2010
title Structure Of The Phage P2 Baseplate In Its Activated Conformation With Ca (Part 2 Of 2)
authors G.Sciara, C.Bebeacua, P.Bron, D.Tremblay, M.Ortiz-Lombardia, J.Lichiere, M.Vanheel, V.Campanacci, S.Moineau, C.Cambillau
compound source
Molecule: Putative Receptor Binding Protein
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R;
Fragment: Residues 2-264
Synonym: Orf18
Engineered: Yes
 Organism_scientific: Lactococcus Phage P2
Organism_taxid: 254252
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector: Pdest17

Molecule: Orf15
Chain: S, T, U, V, W, X
Engineered: Yes
Organism_scientific: Lactococcus Phage P2
Organism_taxid: 254252
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector: Pdest17

Molecule: Orf16
Chain: Y, Z, 0
Engineered: Yes
Organism_scientific: Lactococcus Phage P2
Organism_taxid: 254252
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector: Pdest17
symmetry Space Group: P 1 21 1
R_factor 0.2908 R_Free 0.2974
crystal
cell
length a length b length c angle alpha angle beta angle gamma
219.521 219.337 392.432 90.00 90.02 90.00
method X-Ray Diffractionresolution 5.46 Å
ligand CA enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, Q, M, C, L, A, J, O, P, B, H, D, R, I, G
  • cell adhesion
  • viral infectious cycle
  • viral attachment to host cel...

    • Primary referenceStructure of lactococcal phage p2 baseplate and its mechanism of activation., Sciara G, Bebeacua C, Bron P, Tremblay D, Ortiz-Lombardia M, Lichiere J, van Heel M, Campanacci V, Moineau S, Cambillau C, Proc Natl Acad Sci U S A. 2010 Mar 29. PMID:20351260
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2634 Kb) [Save to disk]
  • Biological Unit Coordinates (2x5a.pdb1.gz) 2626 Kb
  • LPC: Ligand-Protein Contacts for 2X5A
  • CSU: Contacts of Structural Units for 2X5A
  • Structure Factors (638 Kb)
  • Retrieve 2X5A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X5A from S2C, [Save to disk]
    • View 2X5A 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 2X5A
  • 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 2X5A, from MSDmotif at EBI
  • Fold representative 2x5a from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x5a_0] [2x5a_A] [2x5a_B] [2x5a_C] [2x5a_D] [2x5a_E] [2x5a_F] [2x5a_G] [2x5a_H] [2x5a_I] [2x5a_J] [2x5a_K] [2x5a_L] [2x5a_M] [2x5a_N] [2x5a_O] [2x5a_P] [2x5a_Q] [2x5a_R] [2x5a_S] [2x5a_T] [2x5a_U] [2x5a_V] [2x5a_W] [2x5a_X] [2x5a_Y] [2x5a_Z]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2X5A with the sequences similar proteins can be viewed for 2X5A's classification 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 at ProtoMap. Click on the Cluster number.
    • Other resources with information on 2X5A
  • Community annotation for 2X5A 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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