4E1B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

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

  • 2EQA - determined by Agari, Y., Shinkai, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)  

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YrdC/Sua5 family protein
A
352Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Mutation(s): 0 
Gene Names: sua5
EC: 2.7.7.87
Find proteins for Q970S6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q970S6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TXA
Query on TXA

Download SDF File 
Download CCD File 
A
threonylcarbamoyladenylate
C15 H21 N6 O11 P
GHLUPQUHEIJRCU-DWVDDHQFSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.391α = 90.00
b = 120.843β = 90.00
c = 67.552γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
BSSdata collection
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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