3EXC | pdb_00003exc

Structure of the RNA'se SSO8090 from Sulfolobus solfataricus

• PDB DOI: https://doi.org/10.2210/pdb3EXC/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-16 Released: 2008-11-11 
• Deposition Author(s): Singer, A.U., Skarina, T., Tan, K., Kagan, O., Onopriyenko, O., Edwards, A.M., Joachimiak, A., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.221 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Structure of the RNA'se SSO8090 from Sulfolobus solfataricus

Proudfoot, M., Brown, M., Singer, A.U., Skarina, T., Tan, K., Kagan, O., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F.

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)

Macromolecule Content 

• Total Structure Weight: 10.82 kDa 
• Atom Count: 685 
• Modeled Residue Count: 78 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A [auth X]	91	Saccharolobus solfataricus	Mutation(s): 2  Gene Names: SSO8090 EC: 3.1.26 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for Q97Y85 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97Y85  Go to UniProtKB:  Q97Y85

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.221 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.479	α = 90
b = 93.479	β = 90
c = 48.596	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Singer, A.U., Skarina, T., Tan, K., Kagan, O., Onopriyenko, O., Edwards, A.M., Joachimiak, A., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary