6FL1 | pdb_00006fl1

Crystal structure of the complex between the Lactococcus lactis FPG mutant T221P and a Fapy-dG containing DNA

• PDB DOI: https://doi.org/10.2210/pdb6FL1/pdb
• NAKB: 6FL1

• Classification: HYDROLASE
• Organism(s): synthetic construct, Lactococcus cremoris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-25 Released: 2019-02-06 
• Deposition Author(s): Coste, F., Castaing, B., Ober, M., Carell, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.178 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex between the Lactococcus lactis FPG mutant T221P and a Fapy-dG containing DNA

Coste, F., Castaing, B., Ober, M., Carell, T.

To be published.

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: 39.75 kDa 
• Atom Count: 3,220 
• Modeled Residue Count: 299 
• Deposited Residue Count: 299 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Formamidopyrimidine-DNA glycosylase	C [auth A]	271	Lactococcus cremoris	Mutation(s): 1  Gene Names: mutM, fpg, NCDO763_0992 EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*CP*TP*TP*TP(FOX)P*TP*TP*TP*CP*TP*CP*G)-3')	A [auth B]	14	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')	B [auth C]	14	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.178 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.369	α = 90
b = 91.369	β = 90
c = 141.673	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Coste, F., Castaing, B., Ober, M., Carell, T.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description