2GX6

Rational stabilization of E. coli ribose binding protein

• PDB DOI: https://doi.org/10.2210/pdb2GX6/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-05-08 Released: 2007-03-20 
• Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.229 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Rational stabilization of E. coli ribose binding protein

Tian, Y., Cuneo, M.J., Johnson, S., Beese, L.S., Hellinga, H.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.61 kDa 
• Atom Count: 2,298 
• Modelled Residue Count: 271 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ribose-binding periplasmic protein	A	278	Escherichia coli K-12	Mutation(s): 3  Gene Names: rbsB, prlB, rbsP EC: 3.6.3.17
UniProt
Find proteins for P02925 (Escherichia coli (strain K12)) Explore P02925  Go to UniProtKB:  P02925

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIP	B [auth A]	beta-D-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-TXICZTDVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.229 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.847	α = 90
b = 71.05	β = 90
c = 98.949	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references, Structure summary
• Version 1.6: 2023-08-30
  Changes: Data collection, Refinement description