5ILX | pdb_00005ilx

Crystal structure of Ribosome inactivating protein from Momordica balsamina with Uracil at 1.70 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5ILX/pdb
• Entry: 5ILX supersedes: 4FPZ

• Classification: HYDROLASE
• Organism(s): Momordica balsamina
• Mutation(s): No 


• Deposited: 2016-03-05 Released: 2016-03-23 
• Deposition Author(s): Singh, P.K., Singh, A., Pandey, S., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.210 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Ribosome inactivating protein from Momordica balsamina with Uracil at 1.70 Angstrom resolution

Singh, P.K., Singh, A., Pandey, S., Kaur, P., Sharma, S., Singh, T.P.

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: 27.49 kDa 
• Atom Count: 2,194 
• Modeled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome inactivating protein	A	246	Momordica balsamina	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for D9J2T9 (Momordica balsamina) Explore D9J2T9  Go to UniProtKB:  D9J2T9
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
URA	B [auth A]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.210 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.186	α = 90
b = 130.186	β = 90
c = 39.976	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Singh, P.K., Singh, A., Pandey, S., Kaur, P., Sharma, S., Singh, T.P.
• This entry supersedes: 4FPZ

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary