4EQB

1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Transporter Substrate-Binding Protein PotD from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Calcium and HEPES

• PDB DOI: https://doi.org/10.2210/pdb4EQB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae TCH8431/19A
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-04-18 Released: 2012-05-02 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Stogios, P.J., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Transporter Substrate-Binding Protein from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Calcium and HEPES.

Minasov, G., Wawrzak, Z., Stogios, P.J., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., 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 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: 77.27 kDa 
• Atom Count: 6,735 
• Modelled Residue Count: 646 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein	A, B	330	Streptococcus pneumoniae TCH8431/19A	Mutation(s): 0  Gene Names: HMPREF0837_11161

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	H [auth A], O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m34eqb

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.635	α = 75.83
b = 54.347	β = 80.87
c = 76.704	γ = 77.56

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Minasov, G., Wawrzak, Z., Stogios, P.J., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2013-04-17
  Changes: Other
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description