6XTP | pdb_00006xtp

Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Cu:S:O2-1a complex

• PDB DOI: https://doi.org/10.2210/pdb6XTP/pdb

• Classification: TRANSFERASE
• Organism(s): Thermomonospora curvata DSM 43183
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-16 Released: 2021-01-27 
• Deposition Author(s): Leisinger, F., Seebeck, F.P.
• Funding Organization(s): Swiss National Science Foundation, European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.291 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Non-Coordinative Binding of O2 at the Active Center of a Copper-Dependent Enzyme

Leisinger, F., Miarzlou, D.A., Seebeck, F.P.

(2020) Angew Chem Int Ed Engl 

• DOI: https://doi.org/10.1002/ange.202014981

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.02 kDa 
• Atom Count: 2,617 
• Modeled Residue Count: 312 
• Deposited Residue Count: 317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formylglycine-generating enzyme	A	303	Thermomonospora curvata DSM 43183	Mutation(s): 0  Gene Names: Tcur_4811 EC: 1.8.3.7
UniProt
Find proteins for D1A7C3 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A7C3  Go to UniProtKB:  D1A7C3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABZ-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY	B [auth C]	14	Thermomonospora curvata DSM 43183	Mutation(s): 0
UniProt
Find proteins for D1ADF2 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1ADF2  Go to UniProtKB:  D1ADF2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SOA	G [auth C]	ISATOIC ANHYDRIDE C7 H9 N O VYFOAVADNIHPTR-UHFFFAOYSA-N
CU1	C [auth A]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
OXY	F [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.291 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.327	α = 90
b = 70.971	β = 90
c = 75.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Leisinger, F., Seebeck, F.P.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--
European Research Council (ERC)	European Union	ERC-2013- StG 336559

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Advisory, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description