4LAT | pdb_00004lat

Crystal structure of phosphate ABC transporter, periplasmic phosphate-binding protein PstS 1 (PBP1) from Streptococcus pneumoniae Canada MDR_19A in complex with phosphate

• PDB DOI: https://doi.org/10.2210/pdb4LAT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-20 Released: 2013-07-10 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., 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: 1.88 Å
• R-Value Free: 
  0.225 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phosphate ABC transporter, periplasmic phosphate-binding protein PstS 1 (PBP1) from Streptococcus pneumoniae Canada MDR_19A in complex with phosphate

Stogios, P.J., Wawrzak, Z., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F.

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)

Macromolecule Content 

• Total Structure Weight: 28.35 kDa 
• Atom Count: 2,232 
• Modeled Residue Count: 260 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate-binding protein PstS 1	A	265	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: pstS1, SPNECM_010100007640, SP_1400
UniProt
Find proteins for Q97Q31 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97Q31  Go to UniProtKB:  Q97Q31

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.225 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34lat

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.78	α = 90
b = 46.78	β = 90
c = 209.01	γ = 120

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description