1DBP | pdb_00001dbp

IDENTICAL MUTATIONS AT CORRESPONDING POSITIONS IN TWO HOMOLOGOUS PROTEINS WITH NON-IDENTICAL EFFECTS

• PDB DOI: https://doi.org/10.2210/pdb1DBP/pdb

• Classification: BINDING PROTEIN
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1994-01-31 Released: 1994-05-31 
• Deposition Author(s): Mowbray, S.L., Joakim Bjorkman, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.160 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Identical mutations at corresponding positions in two homologous proteins with nonidentical effects.

Bjorkman, A.J., Binnie, R.A., Cole, L.B., Zhang, H., Hermodson, M.A., Mowbray, S.L.

(1994) J Biological Chem 269: 11196-11200

• PubMed: 8157648 
• Primary Citation Related Structures: 
  1DBP


• PubMed Abstract: 
  

  The x-ray structure of a mutant (Gly72 to Asp) of the Escherichia coli ribose-binding protein with altered transport function has been solved and refined to 2.2-A resolution with a conventional R-factor (R-factor = [formula: see text]) of 16.0% and good stereochemistry. Comparison with the wild type ribose-binding protein shows that the structure is disturbed little at the actual mutation site, but quite appreciably in a neighboring loop. Changes in the surface of the protein at the site of mutation, however, seem to explain the functional effects. A corresponding mutation of the related glucose/galactose-binding protein has different structural and functional effects due to the different structural context of the mutation site in that protein. These results are consistent with the concept that these proteins have slightly different ways of interacting with the membrane components in transport and chemotaxis.

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Organizational Affiliation: 
• Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.72 kDa 
• Atom Count: 2,182 
• Modeled Residue Count: 271 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-RIBOSE-BINDING PROTEIN	A	271	Escherichia coli	Mutation(s): 0
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: 2.20 Å
• R-Value Work:  0.160 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.84	α = 90
b = 88.88	β = 90
c = 39.86	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-05-31 
Deposition Author(s): Mowbray, S.L., Joakim Bjorkman, A.J.

Revision History  

• Version 1.0: 1994-05-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Structure summary