1KG5

Crystal structure of the K142Q mutant of E.coli MutY (core fragment)

• PDB DOI: https://doi.org/10.2210/pdb1KG5/pdb

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


• Deposited: 2001-11-26 Released: 2002-11-26 
• Deposition Author(s): Gilboa, R., Kilshtein, A., Zharkov, D.O., Kycia, J.H., Gerchman, S.E., Grollman, A.P., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.169 
• R-Value Work: 0.128 

Starting Model: experimental

Literature

Analysis of the E.coli MutY DNA glycosylase structure and function by site-directed mutagenesis

Gilboa, R., Kilshtein, A., Zharkov, D.O., Kycia, J.H., Gerchman, S.E., Grollman, A.P., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.86 kDa 
• Atom Count: 2,137 
• Modelled Residue Count: 225 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A/G-specific adenine glycosylase	A	225	Escherichia coli	Mutation(s): 1  Gene Names: mutY EC: 3.2.2
UniProt
Find proteins for P17802 (Escherichia coli (strain K12)) Explore P17802  Go to UniProtKB:  P17802

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.169 
• R-Value Work: 0.128 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.49	α = 90
b = 50.12	β = 122.68
c = 70.38	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-26 
Deposition Author(s): Gilboa, R., Kilshtein, A., Zharkov, D.O., Kycia, J.H., Gerchman, S.E., Grollman, A.P., Shoham, G.

Revision History  

• Version 1.0: 2002-11-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-16
  Changes: Data collection, Refinement description