6O1Y | pdb_00006o1y

Structure of pCW3 conjugation coupling protein TcpA monomeric form with ATP

• PDB DOI: https://doi.org/10.2210/pdb6O1Y/pdb

• Classification: TRANSLOCASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-22 Released: 2020-02-26 
• Deposition Author(s): Traore, D.A.K., Ahktar, N., Torres, V.T., Adams, V., Coulibaly, F., Panjikar, S., Caradoc-Davies, T.T., Rood, J.I., Whisstock, J.C.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structure of pCW3 conjugation coupling protein TcpA

Traore, D.A.K., Whisstock, J.C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.56 kDa 
• Atom Count: 5,884 
• Modeled Residue Count: 708 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA translocase coupling protein	A, B	359	Clostridium perfringens	Mutation(s): 0  Gene Names: tcpA, pCW3_0030
UniProt
Find proteins for Q1PLI0 (Clostridium perfringens) Explore Q1PLI0  Go to UniProtKB:  Q1PLI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
BGC	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.453	α = 90
b = 108.663	β = 90
c = 142.384	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Traore, D.A.K., Ahktar, N., Torres, V.T., Adams, V., Coulibaly, F., Panjikar, S., Caradoc-Davies, T.T., Rood, J.I., Whisstock, J.C.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1104502

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary