3DP5

Crystal structure of Geobacter sulfurreducens OmcF with N-terminal Strep-tag II

• PDB DOI: https://doi.org/10.2210/pdb3DP5/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Geobacter sulfurreducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-07 Released: 2008-09-02 
• Deposition Author(s): Lukat, P., Hoffmann, M., Einsle, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Crystal packing of the c(6)-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II

Lukat, P., Hoffmann, M., Einsle, O.

(2008) Acta Crystallogr D Biol Crystallogr 64: 919-926

• PubMed: 18703839 
• DOI: https://doi.org/10.1107/S0907444908021306
• Primary Citation of Related Structures:  
  3DP5


• PubMed Abstract: 
  

  The putative outer membrane c-type cytochrome OmcF from Geobacter sulfurreducens contains a single haem group and shows homology to soluble cytochromes c(6), a class of electron-transfer proteins that are typically found in cyanobacterial photosynthetic electron-transfer chains. OmcF was overexpressed heterologously in Escherichia coli as an N-terminal Strep-tag II fusion protein and isolated using streptactin-affinity chromatography followed by size-exclusion chromatography. The structure was solved by Fe SAD using data collected to a resolution of 1.86 A on a rotating copper-anode X-ray generator. In the crystal, packing interactions in one dimension were exclusively mediated through the Strep-tag II sequence. The tag and linker regions were in contact with three further monomers of OmcF, leading to a well defined electron-density map for this engineered and secondary-structure-free region of the molecule.

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Organizational Affiliation: 

Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.

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: 11.07 kDa 
• Atom Count: 904 
• Modelled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c family protein	A	99	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: GSU2432
UniProt
Find proteins for Q74AE4 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74AE4  Go to UniProtKB:  Q74AE4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.210 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.475	α = 90
b = 40.125	β = 90
c = 42.085	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Lukat, P., Hoffmann, M., Einsle, O.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-10-02
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary