4LMH

Crystal structure of the outer membrane decaheme cytochrome OmcA


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcAA, B, C, D760Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: omcASO_1779
UniProt
Find proteins for Q8EG33 (Shewanella oneidensis (strain MR-1))
Explore Q8EG33 
Go to UniProtKB:  Q8EG33
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth D] , BA [auth B] , BB [auth D] , CA [auth B] , CB [auth D] , DA [auth B] , DB [auth D] , 
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
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
HA [auth B] , IA [auth B] , JA [auth B] , MB [auth D] , NB [auth D] , OB [auth D] , PB [auth D] , Q [auth A] , 
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
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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 = 92.64α = 90
b = 245.38β = 97.89
c = 135.63γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SHELXSphasing
PHENIXrefinement
xia2data reduction
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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