1NIO

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

• PDB DOI: https://doi.org/10.2210/pdb1NIO/pdb

• Classification: HYDROLASE
• Organism(s): Luffa aegyptiaca
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-24 Released: 2003-08-05 
• Deposition Author(s): Wu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

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

• PubMed: 12876337 
• DOI: https://doi.org/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 0.008 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.77 kDa 
• Atom Count: 2,081 
• Modelled Residue Count: 247 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
b-luffin	A	247	Luffa aegyptiaca	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P22851 (Luffa aegyptiaca) Explore P22851  Go to UniProtKB:  P22851
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.902	α = 90
b = 59.823	β = 120.81
c = 55.184	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary