5JJ5 | pdb_00005jj5

Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to hydroxymate siderophore ferrioxamine E and iron(III)

• PDB DOI: https://doi.org/10.2210/pdb5JJ5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-22 Released: 2016-05-04 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kurdritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to hydroxymate siderophore ferrioxamine E and iron(III)

Stogios, P.J.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 69.37 kDa 
• Atom Count: 5,438 
• Modeled Residue Count: 612 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein-iron transport	A, B	308	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: yhfQ, yhfQ_1, yhfQ_2, yhfQ_3
UniProt
Find proteins for A0A062WLD9 (Streptococcus pneumoniae) Explore A0A062WLD9  Go to UniProtKB:  A0A062WLD9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6L0	D [auth A], I [auth B]	(8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone C27 H46 N6 O9 SHTNNSLDUIEFSM-LREOWRDNSA-N
GOL	F [auth A], G [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	C [auth A], H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.809	α = 90
b = 73.844	β = 115.79
c = 87.161	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kurdritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description