6XTM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formylglycine-generating enzyme303Thermomonospora curvata DSM 43183Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1A7C3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Abz-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLYB [auth C]14Thermomonospora curvata DSM 43183Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1ADF2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SOA
Query on SOA

Download Ideal Coordinates CCD File 
J [auth C]ISATOIC ANHYDRIDE
C7 H9 N O
VYFOAVADNIHPTR-UHFFFAOYSA-N
AG
Query on AG

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I [auth A]SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
CA
Query on CA

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D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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F [auth A],
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY
Query on OXY

Download Ideal Coordinates CCD File 
C [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.161α = 90
b = 71.909β = 90
c = 76.769γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
European Research Council (ERC)European UnionERC-2013- StG 336559

Revision History  (Full details and data files)

  • 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