4J65

Crystal structure of Ribonuclease A soaked in 40% Dimethylformamide: One of twelve in MSCS set

• PDB DOI: https://doi.org/10.2210/pdb4J65/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2013-02-11 Released: 2014-01-22 
• Deposition Author(s): Kearney, B.M., Dechene, M., Swartz, P.D., Mattos, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

DRoP: A program for analysis of water structure on protein surfaces

Kearney, B.M., Roberts, D., Dechene, M., Swartz, P.D., Mattos, C.

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: 14.17 kDa 
• Atom Count: 1,048 
• Modelled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMF	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	DIMETHYLFORMAMIDE C3 H7 N O ZMXDDKWLCZADIW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.193 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.208	α = 90
b = 63.208	β = 90
c = 64.682	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Kearney, B.M., Dechene, M., Swartz, P.D., Mattos, C.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary