3DCX

Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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
Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
A, B, C, D, E
117Shewanella loihica (strain ATCC BAA-1088 / PV-4)Mutation(s): 0 
Find proteins for A3QB43 (Shewanella loihica (strain ATCC BAA-1088 / PV-4))
Go to UniProtKB:  A3QB43
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, C, D, E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 61.070α = 90.00
b = 75.320β = 90.00
c = 139.400γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
MolProbitymodel building
PDB_EXTRACTdata extraction
autoSHARPphasing
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-10-10
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence, Refinement description