3N2D

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3N2D/pdb

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


• Deposited: 2010-05-18 Released: 2010-07-28 
• Deposition Author(s): Kushwaha, G.S., Prem Kumar, R., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.222 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution

Kushwaha, G.S., Prem Kumar, R., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.16 kDa 
• Atom Count: 2,171 
• Modelled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-meric peptide from 60S acidic ribosomal protein P2-beta	B	6	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P02400 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02400  Go to UniProtKB:  P02400

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.222 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.186	α = 90
b = 131.186	β = 90
c = 40.734	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Kushwaha, G.S., Prem Kumar, R., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-07-28
  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: 2024-11-06
  Changes: Structure summary