3UF7 | pdb_00003uf7

Co-crystal structure of Escherichia coli uracil-DNA glycosylase and a C-terminal fragement of the single-stranded DNA-binding protein

• PDB DOI: https://doi.org/10.2210/pdb3UF7/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-31 Released: 2012-11-07 
• Deposition Author(s): George, N.P., Liban, T.J., Reyes-Lamothe, R., Keck, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.156 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Identification of the SSB-interaction platform of Escherichia coli uracil-DNA glycosylase

George, N.P., Liban, T.J., Reyes-Lamothe, R., Keck, J.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.41 kDa 
• Atom Count: 2,287 
• Modeled Residue Count: 231 
• Deposited Residue Count: 255 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	237	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2580, JW2564, ung EC: 3.2.2.27
UniProt
Find proteins for P12295 (Escherichia coli (strain K12)) Explore P12295  Go to UniProtKB:  P12295

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	B, C	9	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AGE0 (Escherichia coli (strain K12)) Explore P0AGE0  Go to UniProtKB:  P0AGE0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.156 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.204	α = 90
b = 118.204	β = 90
c = 47.098	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): George, N.P., Liban, T.J., Reyes-Lamothe, R., Keck, J.L.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description