1JY5

RNase-related protein from Calystegia sepium

• PDB DOI: https://doi.org/10.2210/pdb1JY5/pdb

• Classification: HYDROLASE
• Organism(s): Calystegia sepium
• Mutation(s): No 


• Deposited: 2001-09-11 Released: 2002-04-10 
• Deposition Author(s): Rabijns, A., Verboven, C., Rouge, P., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.242 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 

Literature

Structure of an RNase-related protein from Calystegia sepium.

Rabijns, A., Verboven, C., Rouge, P., Barre, A., Van Damme, E.J., Peumans, W.J., De Ranter, C.J.

(2002) Acta Crystallogr D Biol Crystallogr 58: 627-633

• PubMed: 11914487 
• DOI: https://doi.org/10.1107/s090744490200255x
• Primary Citation of Related Structures:  
  1JY5


• PubMed Abstract: 
  

  The structure of a catalytically inactive RNase-related protein from Calystegia sepium (CalsepRRP) has been resolved by protein crystallography at a resolution of 2.05 A and an R factor of 20.74%. Although the protein is completely devoid of ribonuclease activity, it adopts the typical alpha + beta structure of non-base-specific RNases. Analysis of the structure revealed that two amino-acid substitutions in the 'active' P1 site, in combination with the less hydrophobic/aromatic character of the B1 base-recognition site and a completely disrupted B2 base-recognition site, might account for this complete lack of activity.

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Organizational Affiliation: 

Laboratory of Analytical Chemistry and Medicinal Physicochemistry, Faculty of Pharmaceutical Sciences, K. U. Leuven, E. Van Evenstraat 4, B-3000 Leuven, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.8 kDa 
• Atom Count: 3,519 
• Modelled Residue Count: 406 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalsepRRP	A, B	212	Calystegia sepium	Mutation(s): 0
UniProt
Find proteins for Q9M7C7 (Calystegia sepium) Explore Q9M7C7  Go to UniProtKB:  Q9M7C7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.242 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.687	α = 90
b = 121.687	β = 90
c = 66.059	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-10 
Deposition Author(s): Rabijns, A., Verboven, C., Rouge, P., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J.

Revision History  

• Version 1.0: 2002-04-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description