4LWX

Crystal structure of the complex of Ribosome inactivating protein from Momordica Balsamina with peptidoglycan fragment at 1.78 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4LWX/pdb

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


• Deposited: 2013-07-29 Released: 2013-08-28 
• Deposition Author(s): Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.201 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of the complex of Ribosome inactivating protein from Momordica Balsamina with peptidoglycan fragment at 1.78 A resolution

Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.05 kDa 
• Atom Count: 2,211 
• Modelled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA N-glycosidase	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	E [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLN	H [auth A]	GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-VKHMYHEASA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
LAC	F [auth A]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N
ALA	G [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.201 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.239	α = 90
b = 130.239	β = 90
c = 40.113	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations