1DBP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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 Biol Chem 269: 11196-11200

  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-RIBOSE-BINDING PROTEIN271Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02925 (Escherichia coli (strain K12))
Explore P02925 
Go to UniProtKB:  P02925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02925
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RIP
Query on RIP

Download Ideal Coordinates CCD File 
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 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.84α = 90
b = 88.88β = 90
c = 39.86γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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