2HFB | pdb_00002hfb

Crystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2HFB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-06-23 Released: 2007-06-05 
• Deposition Author(s): Paterson, N.G., Riboldi-Tunnicliffe, A., Mitchell, T.J., Isaacs, N.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.290 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.244 (DCC) 

Literature

Crystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae

Paterson, N.G., Riboldi-Tunnicliffe, A., Mitchell, T.J., Isaacs, N.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.75 kDa 
• Atom Count: 6,045 
• Modeled Residue Count: 764 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, sugar-binding protein	A, B	409	Streptococcus pneumoniae TIGR4	Mutation(s): 11  Gene Names: rafE
UniProt
Find proteins for A0A0H2URJ7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URJ7  Go to UniProtKB:  A0A0H2URJ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.290 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.244 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.538	α = 90
b = 144.538	β = 90
c = 224.082	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Paterson, N.G., Riboldi-Tunnicliffe, A., Mitchell, T.J., Isaacs, N.W.

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary