4H5G | pdb_00004h5g

Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 2

• PDB DOI: https://doi.org/10.2210/pdb4H5G/pdb

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


• Deposited: 2012-09-18 Released: 2012-10-03 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kudritska, M., 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: 1.78 Å
• R-Value Free: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 2

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

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: 53.76 kDa 
• Atom Count: 4,262 
• Modeled Residue Count: 480 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC superfamily ATP binding cassette transporter, binding protein	A, B	243	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0  Gene Names: HMPREF0837_11153, SpneCM_010100001092

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	L [auth A], Q [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
PEG	D [auth A], E [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A], J [auth A], K [auth A], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34h5g

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.6	α = 90
b = 183.94	β = 90
c = 62.024	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kudritska, M., Minasov, G., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Other
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description