Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.60 kDa 
• Atom Count: 4608 
• Modelled Residue Count: 521 
• Deposited Residue Count: 550 
• Unique protein chains: 1

1XNF

Crystal structure of E.coli TPR-protein NlpI

• PDB DOI: 10.2210/pdb1XNF/pdb

• Classification: Structural genomics, Unknown function
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-10-04 Released: 2004-11-16 
• Deposition Author(s): Wilson, C.G., Kajander, T., Regan, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

The crystal structure of NlpI. A prokaryotic tetratricopeptide repeat protein with a globular fold.

Wilson, C.G., Kajander, T., Regan, L.

(2005) FEBS J 272: 166-179

• PubMed: 15634341 
• DOI: 10.1111/j.1432-1033.2004.04397.x
• Primary Citation of Related Structures:  
  1XNF


• PubMed Abstract: 
  

There are several different families of repeat proteins. In each, a distinct structural motif is repeated in tandem to generate an elongated structure. The nonglobular, extended structures that result are particularly well suited to present a large surface area and to function as interaction domains. Many repeat proteins have been demonstrated experimentally to fold and function as independent domains. In tetratricopeptide (TPR) repeats, the repeat unit is a helix-turn-helix motif. The majority of TPR motifs occur as three to over 12 tandem repeats in different proteins. The majority of TPR structures in the Protein Data Bank are of isolated domains. Here we present the high-resolution structure of NlpI, the first structure of a complete TPR-containing protein. We show that in this instance the TPR motifs do not fold and function as an independent domain, but are fully integrated into the three-dimensional structure of a globular protein. The NlpI structure is also the first TPR structure from a prokaryote. It is of particular interest because it is a membrane-associated protein, and mutations in it alter septation and virulence.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein nlpI	A, B	275	Escherichia coli	Mutation(s): 3  Gene Names: nlpI
UniProt
Find proteins for P0AFB1 (Escherichia coli (strain K12)) Explore P0AFB1  Go to UniProtKB:  P0AFB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

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: 1.98 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.351	α = 90
b = 81.654	β = 90
c = 136.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-04 
• Released Date: 2004-11-16 
Deposition Author(s): Wilson, C.G., Kajander, T., Regan, L.

Revision History  

• Version 1.0: 2004-11-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance