1YD0

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.167

Literature

Macromolecules
Sequence Display for 1YD0

Classification: DNA BINDING PROTEIN

Total Structure Weight: 11690.23

Macromolecule Entities
Molecule Chains Length Organism Details
UvrABC system protein C A 96 Thermotoga maritima Fragment: N-terminal domain
Gene Name(s): uvrC TM_0265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.167
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 55.01 α = 90.00
b = 55.01 β = 90.00
c = 109.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-23
  • Released Date: 2005-03-01
  • Deposition author(s): Truglio, J.J., Rhau, B., Croteau, D.L., Wang, L., Skorvaga, M., Karakas, E., DellaVecchia, M.J., Wang, H., Van Houten, B., Kisker, C.

Revision History

  • Version 1_0: 2005-03-01

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance