2Y7I

Structural basis for high arginine specificity in Salmonella typhimurium periplasmic binding protein STM4351.

• PDB DOI: https://doi.org/10.2210/pdb2Y7I/pdb

• Classification: ARGININE-BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-01-31 Released: 2011-05-11 
• Deposition Author(s): Stamp, A.L., Owen, P., El Omari, K., Lockyer, M., Lamb, H.K., Charles, I.G., Hawkins, A.R., Stammers, D.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Crystallographic and Microcalorimetric Analyses Reveal the Structural Basis for High Arginine Specificity in the Salmonella Enterica Serovar Typhimurium Periplasmic Binding Protein Stm4351.

Stamp, A.L., Owen, P., El Omari, K., Lockyer, M., Lamb, H.K., Charles, I.G., Hawkins, A.R., Stammers, D.K.

(2011) Proteins 79: 2352

• PubMed: 21560168 
• DOI: https://doi.org/10.1002/prot.23060
• Primary Citation of Related Structures:  
  2Y7I

---

Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 52.19 kDa 
• Atom Count: 3,878 
• Modelled Residue Count: 452 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STM4351	A, B	229	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0
UniProt
Find proteins for Q8ZKA9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKA9  Go to UniProtKB:  Q8ZKA9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	C [auth A], I [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
GOL	H [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
ARG	PDBBind:  2Y7I	Kd: 2900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.317	α = 90
b = 56.331	β = 100.17
c = 88.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Stamp, A.L., Owen, P., El Omari, K., Lockyer, M., Lamb, H.K., Charles, I.G., Hawkins, A.R., Stammers, D.K.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-06-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description