1NIO

Crystal structure of beta-luffin, a ribosome inactivating protein at 2.0A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

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Literature

Crystal structure of beta-luffin, a ribosome-inactivating protein, at 2.0 A resolution.

Ma, Q.J., Li, J.H., Li, H.G., Wu, S., Dong, Y.C.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1366-1370

  • DOI: 10.1107/s0907444903011156
  • Primary Citation of Related Structures:  
    1NIO

  • PubMed Abstract: 

    • The crystal structure of beta-luffin at 2.0 A resolution was solved by the molecular-replacement method using polyalanyl trichosanthin as the search model. The structure was refined with CNS1.1, giving R(work) = 0.162 and R(free) = 0.204. The r.m.s.d.s of the bond lengths and bond angles are 0 ...

    The crystal structure of beta-luffin at 2.0 A resolution was solved by the molecular-replacement method using polyalanyl trichosanthin as the search model. The structure was refined with CNS1.1, giving R(work) = 0.162 and R(free) = 0.204. The r.m.s.d.s of the bond lengths and bond angles are 0.008 A and 1.3 degrees, respectively. The overall structure is similar to those of other type I RIPs. Three N-acetylglucosamine (Nag) molecules are linked to residues Asn2, Asn78 and Asn85 of the protein.

    Organizational Affiliation: 

    Center for Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People's Republic of China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
b-luffinA247Luffa aegyptiacaMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P22851 (Luffa aegyptiaca)
Explore P22851 
Go to UniProtKB:  P22851
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22851
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.902α = 90
b = 59.823β = 120.81
c = 55.184γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2003-08-05 
    • Deposition Author(s): Wu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary