2I58 | pdb_00002i58

Crystal Structure of RafE from Streptococcus pneumoniae complexed with raffinose

• PDB DOI: https://doi.org/10.2210/pdb2I58/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-24 Released: 2007-08-07 
• 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: 2.80 Å
• R-Value Free: 
  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.216 (DCC) 

Starting Model: experimental

Literature

Crystal structure of apo and bound forms 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.

Macromolecule Content 

• Total Structure Weight: 88.01 kDa 
• Atom Count: 6,157 
• Modeled Residue Count: 770 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, sugar-binding protein	A, B	388	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: SP1897
UniProt
Find proteins for A0A0H2URJ7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URJ7  Go to UniProtKB:  A0A0H2URJ7

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose-(1-6)-alpha-D-galactopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan: G40178VU GlyCosmos: G40178VU

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.216 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.214	α = 90
b = 119.435	β = 90
c = 146.326	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Paterson, N.G., Riboldi-Tunnicliffe, A., Mitchell, T.J., Isaacs, N.W.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2020-05-13
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-08-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary