4LMH | pdb_00004lmh

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 (Depositor), 0.223 (DCC)
R-Value Work:
0.193 (Depositor), 0.186 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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
Modeled 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 ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / 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 CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FB [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain N [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain TA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth B] SDF format, chain SA [auth C] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain JB [auth D] SDF format, chain J [auth A] SDF format, chain IB [auth D] SDF format, chain I [auth A] SDF format, chain GB [auth D] SDF format, chain EB [auth D] SDF format, chain E [auth A] SDF format, chain CA [auth B] SDF format, chain BB [auth D] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B]	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 JA [auth B] SDF format, chain OB [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain U [auth B] SDF format, chain S [auth A] SDF format, chain PB [auth D] SDF format, chain NB [auth D] SDF format, chain MB [auth D] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain S [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain S [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain NB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	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 GA [auth B] SDF format, chain LB [auth D] SDF format, chain O [auth A] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain P [auth A] SDF format, chain KB [auth D] SDF format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain LB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain FA [auth B]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.230 (Depositor), 0.223 (DCC)
R-Value Work: 0.193 (Depositor), 0.186 (DCC)
R-Value Observed: 0.195 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Edwards, M.J.

Baiden, N.

Clarke, T.A.

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
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary