5AZA

Crystal structure of MBP-sAglB fusion protein with a 20-residue spacer in the connector helix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report



Literature

Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

Matsuoka, R.Shimada, A.Komuro, Y.Sugita, Y.Kohda, D.

(2016) Protein Sci 25: 754-768

  • DOI: 10.1002/pro.2867
  • Primary Citation of Related Structures:  
    5AZA, 5AZ7, 5AZ6, 5AZ9, 5AZ8

  • PubMed Abstract: 
  • Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these ...

    Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally analyzed. We propose a fusion protein method, to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts in the CCFS. Conventional model building fails when large amplitude motions exist. In this study, the mobile parts appear as smeared electron densities in the CCFS, by suitable processing of the X-ray diffraction data. We applied the CCFS method to a highly mobile presequence peptide bound to the mitochondrial import receptor, Tom20, and a catalytically relevant flexible segment in the oligosaccharyltransferase, AglB. These two examples demonstrated the general applicability of the CCFS method to the analysis of the spatial distribution of motions within protein molecules.


    Organizational Affiliation

    Research Center for Live-Protein Dynamics, Kyushu University, Higashi-Ku, Fukuoka, 812-8582, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related proteinA872Escherichia coli K-12Pyrococcus furiosus COM1
This entity is chimeric
Mutation(s): 1 
Gene Names: malEb4034JW3994
EC: 2.4.99.21
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for I6V0B8 (Pyrococcus furiosus COM1)
Explore I6V0B8 
Go to UniProtKB:  I6V0B8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.468α = 90
b = 100.467β = 90
c = 140.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary