1YTA | pdb_00001yta

Crystal Structure of Oligoribonuclease, the lone essential exoribonuclease in Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1YTA/pdb

• Classification: HYDROLASE,TRANSLATION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-02-10 Released: 2006-02-14 
• Deposition Author(s): Fiedler, T.J., Zuo, Y., Malhotra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.249 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal Structure of Oligoribonuclease, the lone essential exoribonuclease in Escherichia coli

Fiedler, T.J., Zuo, Y., Malhotra, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.72 kDa 
• Atom Count: 6,232 
• Modeled Residue Count: 720 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A, B, C, D	180	Escherichia coli	Mutation(s): 5  Gene Names: ORN EC: 3.1 (PDB Primary Data), 3.1.15 (UniProt)
UniProt
Find proteins for P0A784 (Escherichia coli (strain K12)) Explore P0A784  Go to UniProtKB:  P0A784

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	E [auth A], F [auth A], G [auth B], H [auth C], I [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.249 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 72.87	β = 90
c = 147.76	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Fiedler, T.J., Zuo, Y., Malhotra, A.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary