1R8I

Crystal structure of TraC

• PDB DOI: https://doi.org/10.2210/pdb1R8I/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-24 Released: 2004-01-06 
• Deposition Author(s): Yeo, H.-J., Yuan, Q., Beck, M.R., Baron, C., Waksman, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.288 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 

Literature

Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101

Yeo, H.-J., Yuan, Q., Beck, M.R., Baron, C., Waksman, G.

(2003) Proc Natl Acad Sci U S A 100: 15947-15952

• PubMed: 14673074 
• DOI: https://doi.org/10.1073/pnas.2535211100
• Primary Citation of Related Structures:  
  1R8I


• PubMed Abstract: 
  

  Type IV secretion systems mediate intercellular transfer of macro-molecules via a mechanism ancestrally related to that of bacterial conjugation machineries. TraC of the IncN plasmid pKM101 belongs to the VirB5 family of proteins, an essential component of most type IV secretion systems. Here, we present the structure of TraC. VirB5/TraC is a single domain protein, which consists of a three helix bundle and a loose globular appendage. Structure-based site-directed mutagenesis followed by functional studies indicates that VirB5 proteins participate in protein-protein interactions important for pilus assembly and function.

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Organizational Affiliation: 

Institute of Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.52 kDa 
• Atom Count: 1,368 
• Modelled Residue Count: 187 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TraC	A	213	Escherichia coli	Mutation(s): 0  Gene Names: trac
UniProt
Find proteins for Q9L6G5 (Escherichia coli) Explore Q9L6G5  Go to UniProtKB:  Q9L6G5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.288 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.015	α = 90
b = 144.015	β = 90
c = 91.88	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-06 
Deposition Author(s): Yeo, H.-J., Yuan, Q., Beck, M.R., Baron, C., Waksman, G.

Revision History  

• Version 1.0: 2004-01-06
  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: 2011-09-28
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references