2R8Y Hydrolase date Sep 11, 2007
title Crystal Structure Of Yrbi Phosphatase From Escherichia Coli Complex With Ca
authors O.V.Tsodikov, P.Aggarwal, J.R.Rubin, J.A.Stuckey, R.W.Woodard, T.
compound source
Molecule: Yrbi From Escherichia Coli
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: Bl21
Gene: Yrbi
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B
Expression_system_vector_type: Pet
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.578 156.947 113.991 90.00 96.72 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand CA, CL enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G
  • 3-deoxy-manno-octulosonate-8...


    • Primary referenceThe tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase., Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV, J Biol Chem. 2009 Oct 30;284(44):30594-603. Epub 2009 Sep 2. PMID:19726684
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (446 Kb) [Save to disk]
  • Biological Unit Coordinates (2r8y.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (2r8y.pdb2.gz) 117 Kb
  • Biological Unit Coordinates (2r8y.pdb3.gz) 113 Kb
  • Biological Unit Coordinates (2r8y.pdb4.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 2R8Y
  • CSU: Contacts of Structural Units for 2R8Y
  • Likely Quarternary Molecular Structure file(s) for 2R8Y
  • Structure Factors (1941 Kb)
  • Retrieve 2R8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R8Y from S2C, [Save to disk]
  • Re-refined 2r8y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2R8Y 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 2R8Y
  • 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 2R8Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r8y_K] [2r8y_B] [2r8y_I] [2r8y_F] [2r8y_H] [2r8y_M] [2r8y_D] [2r8y_G] [2r8y_E] [2r8y_A] [2r8y_O] [2r8y_N] [2r8y_C] [2r8y_L] [2r8y] [2r8y_J] [2r8y_P]
  • SWISS-PROT database: [P67653]
  • Domain organization of [KDSC_ECOL6] by SWISSPFAM
    • Other resources with information on 2R8Y
  • Community annotation for 2R8Y 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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