2XWG | pdb_00002xwg

Crystal structure of sortase C-1 from Actinomyces oris (formerly Actinomyces naeslundii)

• PDB DOI: https://doi.org/10.2210/pdb2XWG/pdb

• Classification: HYDROLASE
• Organism(s): Actinomyces oris
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-11-02 Released: 2011-02-23 
• Deposition Author(s): Persson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.244 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of the Sortase Acsrtc-1 from Actinomyces Oris

Persson, K.

(2011) Acta Crystallogr D Biol Crystallogr 67: 212

• PubMed: 21358052 
• DOI: https://doi.org/10.1107/S0907444911004215
• Primary Citation Related Structures: 
  2XWG


• PubMed Abstract: 
  

  The crystal structure of the sortase AcSrtC-1 from the oral microorganism Actinomyces oris has been determined to 2.4 Å resolution. AcSrtC-1 is a cysteine transpeptidase that is responsible for the formation of fimbriae by the polymerization of a shaft protein. Similar to other pili-associated sortases, the AcSrtC-1 active site is protected by a flexible lid. The asymmetric unit contains five AcSrtC-1 molecules and their catalytic Cys-His-Arg triads are trapped in two different conformations. It is also shown that the thermostability of the enzyme is increased by the presence of calcium.

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Organizational Affiliation: 
• Department of Odontology, Umeå University, Umeå, Sweden. [e-mail]

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.82 kDa 
• Atom Count: 7,181 
• Modeled Residue Count: 903 
• Deposited Residue Count: 1,175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SORTASE	A, B, C, D, E	235	Actinomyces oris	Mutation(s): 0
UniProt
Find proteins for Q0Z952 (Actinomyces naeslundii) Explore Q0Z952  Go to UniProtKB:  Q0Z952

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth A], G [auth A], H [auth B], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.244 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.07	α = 90
b = 108.23	β = 90
c = 143.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Persson, K.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description