6ETM | pdb_00006etm

Atomic resolution structure of RNase A (data collection 3)

• PDB DOI: https://doi.org/10.2210/pdb6ETM/pdb

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


• Deposited: 2017-10-27 Released: 2018-02-21 
• Deposition Author(s): Caterino, M., Vergara, A., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.136 (Depositor), 0.122 (DCC) 
• R-Value Work: 
  0.106 (Depositor), 0.099 (DCC) 
• R-Value Observed: 
  0.109 (Depositor) 

Literature

Raman-markers of X-ray radiation damage of proteins.

Vergara, A., Caterino, M., Merlino, A.

(2018) Int J Biol Macromol 111: 1194-1205

• PubMed: 29374529 
• DOI: https://doi.org/10.1016/j.ijbiomac.2018.01.135
• Primary Citation Related Structures: 
  6ETK, 6ETL, 6ETM, 6ETN, 6ETP, 6ETQ, 6ETR


• PubMed Abstract: 
  

  Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy.
Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy. Electronic address: [e-mail].

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: 13.89 kDa 
• Atom Count: 1,396 
• Modeled 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth A], C [auth A], D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.136 (Depositor), 0.122 (DCC) 
• R-Value Work:  0.106 (Depositor), 0.099 (DCC) 
• R-Value Observed: 0.109 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.125	α = 90
b = 37.971	β = 105.83
c = 52.541	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Caterino, M., Vergara, A., Merlino, A.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary