4LMH

Crystal structure of the outer membrane decaheme cytochrome OmcA

• PDB DOI: https://doi.org/10.2210/pdb4LMH/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-10 Released: 2014-04-16 
• Deposition Author(s): Edwards, M.J., Baiden, N., Clarke, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.230 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Insights into electron transfer at the microbe-mineral interface: the X-ray crystal structures of Shewanella oneidensis MtrC and OmcA

Edwards, M.J., Baiden, N., Clarke, T.A., Richardson, D.J.

(2014) Febs Letters 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 352.08 kDa 
• Atom Count: 24,443 
• Modelled Residue Count: 2,774 
• Deposited Residue Count: 3,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA	A, B, C, D	760	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: omcA, SO_1779
UniProt
Find proteins for Q8EG33 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EG33  Go to UniProtKB:  Q8EG33

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], E [auth A], EA [auth B], EB [auth D], F [auth A], FB [auth D], G [auth A], GB [auth D], H [auth A], HB [auth D], I [auth A], IB [auth D], J [auth A], JB [auth D], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
DMS	HA [auth B], IA [auth B], JA [auth B], MB [auth D], NB [auth D], OB [auth D], PB [auth D], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth B], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	FA [auth B], GA [auth B], KB [auth D], LB [auth D], O [auth A], P [auth A], UA [auth C], VA [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.230 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.64	α = 90
b = 245.38	β = 97.89
c = 135.63	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SHELXS	phasing
PHENIX	refinement
xia2	data reduction
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-16 
Deposition Author(s): Edwards, M.J., Baiden, N., Clarke, T.A.

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary