5CE3 | pdb_00005ce3

The Yersinia YopO - actin complex with MgADP

• PDB DOI: https://doi.org/10.2210/pdb5CE3/pdb

• Classification: CONTRACTILE PROTEIN/TRANSFERASE
• Organism(s): Spodoptera frugiperda, Yersinia enterocolitica
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-06 Released: 2016-07-06 
• Deposition Author(s): Lee, W.L., Singaravelu, P., Grimes, J.M., Robinson, R.C.
• Funding Organization(s): Agency for Science, Technology and Research (A*STAR), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

The Yersinia YopO - actin complex with MgADP

Lee, W.L., Grimes, J.M., Robinson, R.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 229.06 kDa 
• Atom Count: 15,121 
• Modeled Residue Count: 1,912 
• Deposited Residue Count: 2,038 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin	A, C	376	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for G3CKA6 (Spodoptera frugiperda) Explore G3CKA6  Go to UniProtKB:  G3CKA6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase YopO	B, D	643	Yersinia enterocolitica	Mutation(s): 5  Gene Names: yopO
UniProt
Find proteins for Q93KQ6 (Yersinia enterocolitica) Explore Q93KQ6  Go to UniProtKB:  Q93KQ6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], I [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	G [auth B], K [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA	F [auth A], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth B], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.73	α = 90
b = 121.75	β = 104.88
c = 118.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Lee, W.L., Singaravelu, P., Grimes, J.M., Robinson, R.C.

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Funding Organization	Location	Grant Number
Agency for Science, Technology and Research (A*STAR)	Singapore	--
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description