2HI8

human formylglycine generating enzyme, C336S mutant, bromide co-crystallization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing the oxygen-binding site of the human formylglycine-generating enzyme using halide ions.

Roeser, D.Schmidt, B.Preusser-Kunze, A.Rudolph, M.G.

(2007) Acta Crystallogr.,Sect.D 63: 621-627

  • DOI: 10.1107/S0907444907009961
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catalytic residue in sulfatases is a unique formylglycine that is post-translationally generated by oxidation of a cysteine or serine precursor. Molecular oxygen oxidizes the cysteine precursor in eukaryotic sulfatases, a reaction that is catalys ...

    The catalytic residue in sulfatases is a unique formylglycine that is post-translationally generated by oxidation of a cysteine or serine precursor. Molecular oxygen oxidizes the cysteine precursor in eukaryotic sulfatases, a reaction that is catalysed by the formylglycine-generating enzyme FGE. Previously, FGE was crystallized in complex with a chloride ion which, based on its similar polarizability and hydrophobicity, indicates the site of molecular oxygen binding. Here, two structures of FGE in complex with bromide and iodide were determined in order to further delineate the volume and stereochemical restraints of the oxygen-binding site for potential reaction intermediates. Anomalous difference density maps unambiguously assigned the nature of the halide ions. Unexpectedly, data collected at a wavelength of 1.54 A from the iodide-containing crystal and data collected at a wavelength of 0.8 A from a bromide-containing crystal were sufficient for SIRAS phasing.


    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
Sulfatase-modifying factor 1
X
286Homo sapiensMutation(s): 1 
Gene Names: SUMF1
EC: 1.8.3.7
Find proteins for Q8NBK3 (Homo sapiens)
Go to Gene View: SUMF1
Go to UniProtKB:  Q8NBK3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CTPSR
P
5Homo sapiensMutation(s): 0 
Gene Names: ARSA
EC: 3.1.6.8
Find proteins for P15289 (Homo sapiens)
Go to Gene View: ARSA
Go to UniProtKB:  P15289
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
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
BR
Query on BR

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Download CCD File 
X
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
X
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.153 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.158α = 90.00
b = 108.792β = 90.00
c = 43.057γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance