5VGC | pdb_00005vgc

Crystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai

• PDB DOI: https://doi.org/10.2210/pdb5VGC/pdb

• Classification: PROTEIN BINDING
• Organism(s): Enterobacteria phage YYZ-2008
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-04-10 Released: 2018-04-18 
• Deposition Author(s): Borek, D., Valleau, D., Skarina, T., Jobin, M.C., Wawrzak, Z., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.297 (Depositor) 
• R-Value Work: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai

Valleau, D., Little, D., Borek, D., Skarina, T., Quaile, A.T., Di Leo, R., Houliston, S., Lemak, A., Arrowsmith, C., Combes, B., Savchenko, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.86 kDa 
• Atom Count: 3,396 
• Modeled Residue Count: 415 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NleG5-1 effector	A, B	214	Enterobacteria phage YYZ-2008	Mutation(s): 1
UniProt
Find proteins for B6DZC0 (Enterobacteria phage YYZ-2008) Explore B6DZC0  Go to UniProtKB:  B6DZC0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth A], K [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A], I [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.297 (Depositor) 
• R-Value Work:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.376	α = 90
b = 151.376	β = 90
c = 87.983	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Borek, D., Valleau, D., Skarina, T., Jobin, M.C., Wawrzak, Z., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Contract No. HHSN272201200026C

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description