4E1B

Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus tokodaii with bound threonylcarbamoyladenylate

• PDB DOI: https://doi.org/10.2210/pdb4E1B/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-06 Released: 2012-03-14 
• Deposition Author(s): Parthier, C., Goerlich, S., Jaenecke, F., Breithaupt, C., Braeuer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Boettcher, C., Scheel, D., Stubbs, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2EQA

Literature

The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.

Parthier, C., Gorlich, S., Jaenecke, F., Breithaupt, C., Brauer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Bottcher, C., Scheel, D., Stubbs, M.T.

(2012) Angew Chem Int Ed Engl 51: 4046-4052

• PubMed: 22383337 
• DOI: https://doi.org/10.1002/anie.201108896
• Primary Citation of Related Structures:  
  3VEN, 3VEO, 3VER, 3VES, 3VET, 3VEW, 3VEX, 3VEZ, 3VF2, 3VF4, 4E1B

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Organizational Affiliation: 

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.

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: 39.6 kDa 
• Atom Count: 2,776 
• Modelled Residue Count: 330 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YrdC/Sua5 family protein	A	352	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: STK_15260, SUA5
UniProt
Find proteins for Q970S6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970S6  Go to UniProtKB:  Q970S6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TXA	C [auth A]	threonylcarbamoyladenylate C15 H21 N6 O11 P GHLUPQUHEIJRCU-DWVDDHQFSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.391	α = 90
b = 120.843	β = 90
c = 67.552	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
SOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Parthier, C., Goerlich, S., Jaenecke, F., Breithaupt, C., Braeuer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Boettcher, C., Scheel, D., Stubbs, M.T.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Database references