3R3R | pdb_00003r3r

Structure of the YrdA ferripyochelin binding protein from Salmonella enterica

• PDB DOI: https://doi.org/10.2210/pdb3R3R/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-16 Released: 2011-03-30 
• Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.160 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Structure of the YrdA ferripyochelin binding protein from Salmonella enterica

Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.36 kDa 
• Atom Count: 1,850 
• Modeled Residue Count: 184 
• Deposited Residue Count: 187 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ferripyochelin binding protein	A	187	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: yrdA, STM3399
UniProt
Find proteins for Q8ZLN3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZLN3  Go to UniProtKB:  Q8ZLN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.160 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33r3r

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.43	α = 90
b = 99.43	β = 90
c = 46.66	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-30 
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations