4Q29

Ensemble Refinement of plu4264 protein from Photorhabdus luminescens

• PDB DOI: https://doi.org/10.2210/pdb4Q29/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Photorhabdus laumondii subsp. laumondii TTO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-07 Released: 2014-05-07 
• Deposition Author(s): Wang, F., Michalska, K., Li, H., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Yennamalli, R., Weerth, S., Miller, M.D., Thomas, M.G., Joachimiak, A., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.155 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 

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

• PubMed: 25354690 
• DOI: https://doi.org/10.1002/prot.24705
• Primary Citation of Related Structures:  
  4MV2, 4Q29


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.28 kDa 
• Atom Count: 2,535 
• Modelled Residue Count: 241 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
plu4264 protein	A, B	128	Photorhabdus laumondii subsp. laumondii TTO1	Mutation(s): 0  Gene Names: plu4264
UniProt
Find proteins for Q7MZL9 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)) Explore Q7MZL9  Go to UniProtKB:  Q7MZL9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.155 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.738	α = 90
b = 147.687	β = 90
c = 83.843	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Wang, F., Michalska, K., Li, H., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Yennamalli, R., Weerth, S., Miller, M.D., Thomas, M.G., Joachimiak, A., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Database references
• Version 1.2: 2015-02-11
  Changes: Database references