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.

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

Ligand Structure Quality Assessment

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 MR-1)) Explore Q8EG33 Go to UniProtKB: Q8EG33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8EG33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain F [auth A] SDF format, chain FB [auth D] SDF format, chain G [auth A] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain CB [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain CB [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] 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		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain JA [auth B] SDF format, chain MB [auth D] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth B] SDF format, chain WA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain IA [auth B] SDF format, chain NB [auth D] SDF format, chain S [auth A] SDF format, chain XA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain XA [auth C]	HA [auth B] IA [auth B] JA [auth B] MB [auth D] NB [auth D] 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		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain KB [auth D] SDF format, chain LB [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain UA [auth C] SDF format, chain VA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C]	FA [auth B] GA [auth B] KB [auth D] LB [auth D] O [auth A] 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		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain UA [auth C] Focus chain VA [auth C]