4M5A | pdb_00004m5a

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina inhibited by asymmetric dimethyl arginine at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4M5A/pdb

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


• Deposited: 2013-08-08 Released: 2013-08-28 
• Deposition Author(s): Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Bhushan, A., 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: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina inhibited by asymmetric dimethyl arginine at 1.70 A resolution

Yamini, S., Pandey, S., Kushwaha, G.S., Sinha, M., Bhushan, A., 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: 27.52 kDa 
• Atom Count: 2,172 
• Modeled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
DA2	C [auth A]	NG,NG-DIMETHYL-L-ARGININE C8 H18 N4 O2 YDGMGEXADBMOMJ-LURJTMIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.257	α = 90
b = 130.257	β = 90
c = 39.74	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., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-11-06
  Changes: Non-polymer description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary