Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.97 kDa 
• Atom Count: 720 
• Modelled Residue Count: 87 
• Deposited Residue Count: 105 
• Unique protein chains: 1

1PFP

CATHELIN-LIKE MOTIF OF PROTEGRIN-3

• DOI: 10.2210/pdb1PFP/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-27 Released: 2003-11-11 
• Deposition Author(s): Strub, M.-P., Hoh, F., Sanchez, J.-F., Strub, J.M., Bock, A., Aumelas, A., Dumas, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.219 
• R-Value Observed: 0.227 

Literature

Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing

Strub, M.-P., Hoh, F., Sanchez, J.-F., Strub, J.M., Bock, A., Aumelas, A., Dumas, C.

(2003) Structure 11: 1359-1367

• PubMed: 14604526 
• DOI: 10.1016/j.str.2003.09.014
• Primary Citation of Related Structures:  
  1PAE, 1PFP


• PubMed Abstract: 
  

A protocol for the quantitative incorporation of both selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli is described. This methodology is based on the use of a suitable cysteine auxotrophic strain and a minimal medium supplemented with selenium-labeled methionine and cysteine. The proteins chosen for these studies are the cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase. Analysis of the purified proteins by electrospray mass spectrometry and X-ray crystallography revealed that both cysteine and methionine residues were isomorphously replaced by selenocysteine and selenomethionine. Moreover, selenocysteines allowed the formation of unstrained and stable diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This novel selenium double-labeling method is proposed as a general approach to increase the efficiency of the MAD technique used for phase determination in protein crystallography.

---

Related Citations: 

• Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein.
  Sanchez, J.-F., Hoh, F., Strub, M.-P., Aumelas, A., Dumas, C.
  (2002) Structure 10: 1363

---

Organizational Affiliation: 

Centre de Biochimie Structurale, UMR CNRS 5048, UMR 554 INSERM, Université Montpellier I, 34090 Cedex, Montpellier, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protegrin 3	A	105	Sus scrofa	Mutation(s): 4  Gene Names: NPG3
Find proteins for P32196 (Sus scrofa) Explore P32196  Go to UniProtKB:  P32196

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.219 
• R-Value Observed: 0.227 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.541	α = 90
b = 51.541	β = 90
c = 134.512	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-27 
• Released Date: 2003-11-11 
Deposition Author(s): Strub, M.-P., Hoh, F., Sanchez, J.-F., Strub, J.M., Bock, A., Aumelas, A., Dumas, C.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-02-19
  Changes: Atomic model, Structure summary
• Version 1.4: 2014-08-06
  Changes: Derived calculations, Structure summary