4I62 | pdb_00004i62

1.05 Angstrom crystal structure of an amino acid ABC transporter substrate-binding protein AbpA from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine

• PDB DOI: https://doi.org/10.2210/pdb4I62/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae str. Canada MDR_19A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-29 Released: 2012-12-12 
• Deposition Author(s): Stogios, P.J., Kudritska, M., Wawrzak, Z., Minasov, G., 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: 1.05 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

1.05 Angstrom crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine

Stogios, P.J., Kudritska, M., Wawrzak, Z., Minasov, G., 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)

Macromolecule Content 

• Total Structure Weight: 29.55 kDa 
• Atom Count: 2,399 
• Modeled Residue Count: 237 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter, periplasmic amino acid-binding protein, putative	A	269	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0  Gene Names: SpneCM_010100008960
UniProt
Find proteins for A0A0H2ZN67 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZN67  Go to UniProtKB:  A0A0H2ZN67

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	B [auth A]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34i62

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.682	α = 90
b = 55.028	β = 114.09
c = 46.673	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Stogios, P.J., Kudritska, M., Wawrzak, Z., Minasov, G., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2013-04-17
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description