4GNR | pdb_00004gnr

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

• PDB DOI: https://doi.org/10.2210/pdb4GNR/pdb

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


• Deposited: 2012-08-17 Released: 2012-09-05 
• Deposition Author(s): Halavaty, A.S., Kudritska, M., Wawrzak, Z., Stogios, P.J., 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: 1.00 Å
• R-Value Free: 
  0.147 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

Literature

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

Halavaty, A.S., Kudritska, M., Wawrzak, Z., Stogios, P.J., 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: 37.46 kDa 
• Atom Count: 3,601 
• Modeled Residue Count: 348 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein-branched chain amino acid transport	A	353	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0
UniProt
Find proteins for J9PBT7 (Streptococcus pneumoniae str. Canada MDR_19A) Explore J9PBT7  Go to UniProtKB:  J9PBT7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ILE	B [auth A]	ISOLEUCINE C6 H13 N O2 AGPKZVBTJJNPAG-WHFBIAKZSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.147 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34gnr

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.274	α = 90
b = 72.819	β = 105.1
c = 57.542	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Halavaty, A.S., Kudritska, M., Wawrzak, Z., Stogios, P.J., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

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