4MV2

Crystal structure of plu4264 protein from Photorhabdus luminescens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.349 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 angstrom resolution.

Weerth, R.S.Michalska, K.Bingman, C.A.Yennamalli, R.M.Li, H.Jedrzejczak, R.Wang, F.Babnigg, G.Joachimiak, A.Thomas, M.G.Phillips, G.N.

(2015) Proteins 83: 383-388

  • DOI: 10.1002/prot.24705
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins belonging to the cupin superfamily have a wide range of catalytic and noncatalytic functions. Cupin proteins commonly have the capacity to bind a metal ion with the metal frequently determining the function of the protein. We have been inves ...

    Proteins belonging to the cupin superfamily have a wide range of catalytic and noncatalytic functions. Cupin proteins commonly have the capacity to bind a metal ion with the metal frequently determining the function of the protein. We have been investigating the function of homologous cupin proteins that are conserved in more than 40 species of bacteria. To gain insights into the potential function of these proteins we have solved the structure of Plu4264 from Photorhabdus luminescens TTO1 at a resolution of 1.35 Å and identified manganese as the likely natural metal ligand of the protein.


    Organizational Affiliation

    Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
plu4264
A, B
128Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)Mutation(s): 0 
Find proteins for Q7MZL9 (Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Go to UniProtKB:  Q7MZL9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.349 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.136 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 55.738α = 90.00
b = 147.687β = 90.00
c = 83.843γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
HKL-3000data scaling
SHELXphasing
ARP/wARPmodel building
DMmodel building
SBC-Collectdata collection
MLPHAREphasing
DMphasing
Cootmodel building
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Source and taxonomy
  • Version 1.2: 2014-11-12
    Type: Database references
  • Version 1.3: 2015-02-04
    Type: Database references