1Z70

1.15A resolution structure of the formylglycine generating enzyme FGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

De novo calcium/sulfur SAD phasing of the human formylglycine-generating enzyme using in-house data.

Roeser, D.Dickmanns, A.Gasow, K.Rudolph, M.G.

(2005) Acta Crystallogr.,Sect.D 61: 1057-1066

  • DOI: 10.1107/S0907444905013831

  • PubMed Abstract: 
  • Sulfatases are a family of enzymes essential for the degradation of sulfate esters. Formylglycine is the key catalytic residue in the active site of sulfatases and is generated from a cysteine residue by FGE, the formylglycine-generating enzyme. Inac ...

    Sulfatases are a family of enzymes essential for the degradation of sulfate esters. Formylglycine is the key catalytic residue in the active site of sulfatases and is generated from a cysteine residue by FGE, the formylglycine-generating enzyme. Inactivity of FGE owing to inherited mutations in the FGE gene results in multiple sulfatase deficiency (MSD), which leads to early death in infants. Human FGE was crystallized in the presence of traces of the protease elastase, which was absolutely essential for crystal growth, and the structure of FGE was determined by molecular replacement. Before this model was completed, the FGE structure was re-determined by SAD phasing using in-house data based on the anomalous signal of two calcium ions bound to the native enzyme and intrinsic S atoms. A 14-atom substructure was determined at 1.8 A resolution by SHELXD; SHELXE was used for density modification and phase extension to 1.54 A resolution. Automated model building with ARP/wARP and refinement with REFMAC5 yielded a virtually complete model without manual intervention. The minimal data requirements for successful phasing and the relative contributions of the Ca and S atoms are discussed and compared with the related FGE paralogue, pFGE. This work emphasizes the usefulness of de novo phasing using weak anomalous scatterers and in-house data.


    Organizational Affiliation

    Department of Molecular Structural Biology, University of Göttingen, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-alpha-formyglycine-generating enzyme
X
311Homo sapiensMutation(s): 0 
Gene Names: SUMF1
EC: 1.8.3.7
Find proteins for Q8NBK3 (Homo sapiens)
Go to Gene View: SUMF1
Go to UniProtKB:  Q8NBK3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

Download SDF File 
Download CCD File 
X
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
X
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
X
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.295α = 90.00
b = 109.765β = 90.00
c = 43.511γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-03-23 
  • Released Date: 2005-07-22 
  • Deposition Author(s): Rudolph, M.G.

Revision History 

  • Version 1.0: 2005-07-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance