3RTJ

Crystal structure of ricin bound with dinucleotide ApG

• PDB DOI: https://doi.org/10.2210/pdb3RTJ/pdb
• Entry: 3RTJ supersedes: 1APG
• NAKB: 3RTJ

• Classification: HYDROLASE/RNA
• Organism(s): Ricinus communis
• Mutation(s): No 


• Deposited: 2011-05-03 Released: 2011-08-31 
• Deposition Author(s): Monzingo, A.F., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 0.198 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61.09 kDa 
• Atom Count: 4,189 
• Modelled Residue Count: 522 
• Deposited Residue Count: 531 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain	B [auth A]	267	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin B chain	C [auth B]	262	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*G)-3')	A [auth D]	2	N/A

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	D [auth C], E	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	D [auth C], E	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.74	α = 90
b = 78.49	β = 90
c = 114.34	γ = 90

Software Package:

Software Name	Purpose
San	data collection
X-PLOR	model building
X-PLOR	refinement
San	data reduction
San	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Monzingo, A.F., Robertus, J.D.
• This entry supersedes: 1APG

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary