3NFM | pdb_00003nfm

Crystal Structure of the complex of type I ribosome inactivating protein with fructose at 2.5A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NFM/pdb

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


• Deposited: 2010-06-10 Released: 2010-06-30 
• Deposition Author(s): Kushwaha, G.S., Pandey, N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the complex of type I ribosome inactivating protein with fructose at 2.5A 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: 27.79 kDa 
• Atom Count: 2,063 
• 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
FRU	C [auth A]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.85	α = 90
b = 129.85	β = 90
c = 40.42	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: 2010-06-30 
Deposition Author(s): Kushwaha, G.S., Pandey, N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-06-30
  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