2HEU

Atomic resolution structure of apo-form of RafE from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2HEU/pdb

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


• Deposited: 2006-06-22 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: 1.04 Å
• R-Value Free: 0.157 
• R-Value Work: 0.130 
• R-Value Observed: 0.131 

Literature

High resolution crystal structures of 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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 135.69 kDa 
• Atom Count: 12,875 
• Modelled Residue Count: 1,171 
• Deposited Residue Count: 1,203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, sugar-binding protein	A, B, C	401	Streptococcus pneumoniae	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	I [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.157 
• R-Value Work: 0.130 
• R-Value Observed: 0.131 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.219	α = 90
b = 129.315	β = 94.21
c = 119.42	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection

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: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.5: 2024-05-29
  Changes: Data collection