3B77

Crystal structure of a ph domain containing bacterial protein (exig_2160) from exiguobacterium sibiricum 255-15 at 2.42 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.

Xu, Q.Bateman, A.Finn, R.D.Abdubek, P.Astakhova, T.Axelrod, H.L.Bakolitsa, C.Carlton, D.Chen, C.Chiu, H.J.Chiu, M.Clayton, T.Das, D.Deller, M.C.Duan, L.Ellrott, K.Ernst, D.Farr, C.L.Feuerhelm, J.Grant, J.C.Grzechnik, A.Han, G.W.Jaroszewski, L.Jin, K.K.Klock, H.E.Knuth, M.W.Kozbial, P.Krishna, S.S.Kumar, A.Marciano, D.McMullan, D.Miller, M.D.Morse, A.T.Nigoghossian, E.Nopakun, A.Okach, L.Puckett, C.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.J.Trame, C.B.van den Bedem, H.Weekes, D.Wooten, T.Hodgson, K.O.Wooley, J.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2010) J.Mol.Biol. 396: 31-46

  • DOI: 10.1016/j.jmb.2009.11.006
  • Primary Citation of Related Structures:  3DCX, 3HSA

  • PubMed Abstract: 
  • Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existenc ...

    Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C(5) symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C(12) symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.


    Organizational Affiliation

    Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B, C, D, E, F
193Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15)N/A
Find proteins for B1YJX4 (Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15))
Go to UniProtKB:  B1YJX4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 150.990α = 90.00
b = 150.990β = 90.00
c = 76.219γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
ADSCdata collection
PHENIXrefinement
XSCALEdata scaling
SHELXDphasing
MolProbitymodel building
SHELXphasing
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description