2G5X | pdb_00002g5x

Crystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP)

• PDB DOI: https://doi.org/10.2210/pdb2G5X/pdb

• Classification: HYDROLASE
• Organism(s): Silene chalcedonica
• Mutation(s): No 


• Deposited: 2006-02-23 Released: 2007-03-06 
• Deposition Author(s): Fermani, S., Falini, G., Tosi, G., Ripamonti, A., Polito, L., Bolognesi, A., Stirpe, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP)

Fermani, S., Falini, G., Tosi, G., Ripamonti, A., Polito, L., Bolognesi, A., Stirpe, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.16 kDa 
• Atom Count: 2,227 
• Modeled Residue Count: 234 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-inactivating protein	A	234	Silene chalcedonica	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P85101 (Silene chalcedonica) Explore P85101  Go to UniProtKB:  P85101

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.247	α = 90
b = 57.333	β = 106.25
c = 53.23	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Fermani, S., Falini, G., Tosi, G., Ripamonti, A., Polito, L., Bolognesi, A., Stirpe, F.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary