3MRY | pdb_00003mry

Crystal Structure of type I ribosome inactivating protein from Momordica balsamina with 6-aminopurine at 2.0A resolution

• PDB DOI: https://doi.org/10.2210/pdb3MRY/pdb

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


• Deposited: 2010-04-29 Released: 2010-06-23 
• Deposition Author(s): Kushwaha, G.S., Pandey, N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of type I ribosome inactivating protein from Momordica balsamina with 6-aminopurine at 2.0A resolution

Kushwaha, G.S., Pandey, N., 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: 27.72 kDa 
• Atom Count: 2,126 
• 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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	C [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.135	α = 90
b = 130.135	β = 90
c = 39.524	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: 2010-06-23 
Deposition Author(s): Kushwaha, G.S., Pandey, N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary