5DA5 | pdb_00005da5

Crystal structure of Rhodospirillum rubrum Rru_A0973

PDB DOI: https://doi.org/10.2210/pdb5DA5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodospirillum rubrum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-19 Released: 2016-08-10
Deposition Author(s): He, D., Vanden Hehier, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.
Funding Organization(s): China Scholarships Council, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.206 (Depositor), 0.203 (DCC)
R-Value Work:
0.171 (Depositor), 0.167 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments.

He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E.J., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

(2016) Elife 5

PubMed: 27529188 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.18972
Primary Citation Related Structures:
5DA5, 5L89, 5L8B, 5L8G

PubMed Abstract:
Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an encapsulin capsid. We show that this encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent manner to form a ferroxidase center at a dimer interface. EncFtn adopts an open decameric structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and represents a distinct class of iron storage system, where the oxidation and mineralization of iron are distributed between two proteins.

Organizational Affiliation

Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.

Macromolecule Content

Total Structure Weight: 404.44 kDa
Atom Count: 23,222
Modeled Residue Count: 2,703
Deposited Residue Count: 3,480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rru_A0973	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	116	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: Rru_A0973 EC: 1.16.3.1
UniProt
Find proteins for Q2RVS1 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RVS1 Go to UniProtKB: Q2RVS1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2RVS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOA Query on GOA Download:Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain AC [auth Q] SDF format, chain FA [auth A] SDF format, chain FC [auth U] SDF format, chain HC [auth V] SDF format, chain LA [auth B] SDF format, chain PA [auth D] SDF format, chain QB [auth N] SDF format, chain VA [auth F] SDF format, chain XC [auth a] SDF format, chain VB [auth P] SDF format, chain QC [auth Z] SDF format, chain MC [auth X] SDF format, chain MA [auth C] SDF format, chain KB [auth L] SDF format, chain IB [auth K] MOL2 format, chain AB [auth G] MOL2 format, chain AC [auth Q] MOL2 format, chain FA [auth A] MOL2 format, chain FC [auth U] MOL2 format, chain HC [auth V] MOL2 format, chain LA [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain QB [auth N] MOL2 format, chain VA [auth F] MOL2 format, chain XC [auth a] MOL2 format, chain VB [auth P] MOL2 format, chain QC [auth Z] MOL2 format, chain MC [auth X] MOL2 format, chain MA [auth C] MOL2 format, chain KB [auth L] MOL2 format, chain IB [auth K] mmCIF format, chain AB [auth G] mmCIF format, chain AC [auth Q] mmCIF format, chain FA [auth A] mmCIF format, chain FC [auth U] mmCIF format, chain HC [auth V] mmCIF format, chain LA [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain QB [auth N] mmCIF format, chain VA [auth F] mmCIF format, chain XC [auth a] mmCIF format, chain VB [auth P] mmCIF format, chain QC [auth Z] mmCIF format, chain MC [auth X] mmCIF format, chain MA [auth C] mmCIF format, chain KB [auth L] mmCIF format, chain IB [auth K]	AB [auth G] AC [auth Q] FA [auth A] FC [auth U] HC [auth V] AB [auth G], AC [auth Q], FA [auth A], FC [auth U], HC [auth V], IB [auth K], KB [auth L], LA [auth B], MA [auth C], MC [auth X], PA [auth D], QB [auth N], QC [auth Z], VA [auth F], VB [auth P], XC [auth a]	GLYCOLIC ACID C₂ H₄ O₃ AEMRFAOFKBGASW-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain AC [auth Q] Focus chain FA [auth A] Focus chain FC [auth U] Focus chain HC [auth V] Focus chain IB [auth K] Focus chain KB [auth L] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain MC [auth X] Focus chain PA [auth D] Focus chain QB [auth N] Focus chain QC [auth Z] Focus chain VA [auth F] Focus chain VB [auth P] Focus chain XC [auth a] Interactions & Density Focus chain AB [auth G] Focus chain AC [auth Q] Focus chain FA [auth A] Focus chain FC [auth U] Focus chain HC [auth V] Focus chain IB [auth K] Focus chain KB [auth L] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain MC [auth X] Focus chain PA [auth D] Focus chain QB [auth N] Focus chain QC [auth Z] Focus chain VA [auth F] Focus chain VB [auth P] Focus chain XC [auth a]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain CC [auth U] SDF format, chain EA [auth A] SDF format, chain FB [auth K] SDF format, chain GC [auth V] SDF format, chain HA [auth A] SDF format, chain HB [auth K] SDF format, chain LC [auth X] SDF format, chain OB [auth L] SDF format, chain PB [auth N] SDF format, chain TC [auth a] SDF format, chain UA [auth F] SDF format, chain ZA [auth G] SDF format, chain ZB [auth Q] SDF format, chain YB [auth Q] SDF format, chain XB [auth P] SDF format, chain XA [auth F] SDF format, chain WC [auth a] SDF format, chain UB [auth P] SDF format, chain SC [auth Z] SDF format, chain SB [auth N] SDF format, chain SA [auth D] SDF format, chain PC [auth Z] SDF format, chain OC [auth X] SDF format, chain OA [auth D] SDF format, chain KC [auth V] SDF format, chain KA [auth B] SDF format, chain JB [auth L] SDF format, chain IA [auth B] SDF format, chain EC [auth U] MOL2 format, chain CB [auth G] MOL2 format, chain CC [auth U] MOL2 format, chain EA [auth A] MOL2 format, chain FB [auth K] MOL2 format, chain GC [auth V] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth K] MOL2 format, chain LC [auth X] MOL2 format, chain OB [auth L] MOL2 format, chain PB [auth N] MOL2 format, chain TC [auth a] MOL2 format, chain UA [auth F] MOL2 format, chain ZA [auth G] MOL2 format, chain ZB [auth Q] MOL2 format, chain YB [auth Q] MOL2 format, chain XB [auth P] MOL2 format, chain XA [auth F] MOL2 format, chain WC [auth a] MOL2 format, chain UB [auth P] MOL2 format, chain SC [auth Z] MOL2 format, chain SB [auth N] MOL2 format, chain SA [auth D] MOL2 format, chain PC [auth Z] MOL2 format, chain OC [auth X] MOL2 format, chain OA [auth D] MOL2 format, chain KC [auth V] MOL2 format, chain KA [auth B] MOL2 format, chain JB [auth L] MOL2 format, chain IA [auth B] MOL2 format, chain EC [auth U] mmCIF format, chain CB [auth G] mmCIF format, chain CC [auth U] mmCIF format, chain EA [auth A] mmCIF format, chain FB [auth K] mmCIF format, chain GC [auth V] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth K] mmCIF format, chain LC [auth X] mmCIF format, chain OB [auth L] mmCIF format, chain PB [auth N] mmCIF format, chain TC [auth a] mmCIF format, chain UA [auth F] mmCIF format, chain ZA [auth G] mmCIF format, chain ZB [auth Q] mmCIF format, chain YB [auth Q] mmCIF format, chain XB [auth P] mmCIF format, chain XA [auth F] mmCIF format, chain WC [auth a] mmCIF format, chain UB [auth P] mmCIF format, chain SC [auth Z] mmCIF format, chain SB [auth N] mmCIF format, chain SA [auth D] mmCIF format, chain PC [auth Z] mmCIF format, chain OC [auth X] mmCIF format, chain OA [auth D] mmCIF format, chain KC [auth V] mmCIF format, chain KA [auth B] mmCIF format, chain JB [auth L] mmCIF format, chain IA [auth B] mmCIF format, chain EC [auth U]	CB [auth G] CC [auth U] EA [auth A] EC [auth U] FB [auth K] CB [auth G], CC [auth U], EA [auth A], EC [auth U], FB [auth K], GC [auth V], HA [auth A], HB [auth K], IA [auth B], JB [auth L], KA [auth B], KC [auth V], LC [auth X], OA [auth D], OB [auth L], OC [auth X], PB [auth N], PC [auth Z], SA [auth D], SB [auth N], SC [auth Z], TC [auth a], UA [auth F], UB [auth P], WC [auth a], XA [auth F], XB [auth P], YB [auth Q], ZA [auth G], ZB [auth Q]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain CC [auth U] Focus chain EA [auth A] Focus chain EC [auth U] Focus chain FB [auth K] Focus chain GC [auth V] Focus chain HA [auth A] Focus chain HB [auth K] Focus chain IA [auth B] Focus chain JB [auth L] Focus chain KA [auth B] Focus chain KC [auth V] Focus chain LC [auth X] Focus chain OA [auth D] Focus chain OB [auth L] Focus chain OC [auth X] Focus chain PB [auth N] Focus chain PC [auth Z] Focus chain SA [auth D] Focus chain SB [auth N] Focus chain SC [auth Z] Focus chain TC [auth a] Focus chain UA [auth F] Focus chain UB [auth P] Focus chain WC [auth a] Focus chain XA [auth F] Focus chain XB [auth P] Focus chain YB [auth Q] Focus chain ZA [auth G] Focus chain ZB [auth Q] Interactions & Density Focus chain CB [auth G] Focus chain CC [auth U] Focus chain EA [auth A] Focus chain EC [auth U] Focus chain FB [auth K] Focus chain GC [auth V] Focus chain HA [auth A] Focus chain HB [auth K] Focus chain IA [auth B] Focus chain JB [auth L] Focus chain KA [auth B] Focus chain KC [auth V] Focus chain LC [auth X] Focus chain OA [auth D] Focus chain OB [auth L] Focus chain OC [auth X] Focus chain PB [auth N] Focus chain PC [auth Z] Focus chain SA [auth D] Focus chain SB [auth N] Focus chain SC [auth Z] Focus chain TC [auth a] Focus chain UA [auth F] Focus chain UB [auth P] Focus chain WC [auth a] Focus chain XA [auth F] Focus chain XB [auth P] Focus chain YB [auth Q] Focus chain ZA [auth G] Focus chain ZB [auth Q]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain DB [auth I] SDF format, chain DC [auth U] SDF format, chain EB [auth J] SDF format, chain GB [auth K] SDF format, chain JC [auth V] SDF format, chain LB [auth L] SDF format, chain MB [auth L] SDF format, chain NB [auth L] SDF format, chain NC [auth X] SDF format, chain QA [auth D] SDF format, chain RB [auth N] SDF format, chain TB [auth N] SDF format, chain UC [auth a] SDF format, chain VC [auth a] SDF format, chain YA [auth F] SDF format, chain YC [auth a] SDF format, chain ZC [auth c] SDF format, chain WB [auth P] SDF format, chain WA [auth F] SDF format, chain TA [auth D] SDF format, chain RC [auth Z] SDF format, chain RA [auth D] SDF format, chain NA [auth C] SDF format, chain JA [auth B] SDF format, chain IC [auth V] SDF format, chain GA [auth A] SDF format, chain BC [auth Q] MOL2 format, chain BB [auth G] MOL2 format, chain DB [auth I] MOL2 format, chain DC [auth U] MOL2 format, chain EB [auth J] MOL2 format, chain GB [auth K] MOL2 format, chain JC [auth V] MOL2 format, chain LB [auth L] MOL2 format, chain MB [auth L] MOL2 format, chain NB [auth L] MOL2 format, chain NC [auth X] MOL2 format, chain QA [auth D] MOL2 format, chain RB [auth N] MOL2 format, chain TB [auth N] MOL2 format, chain UC [auth a] MOL2 format, chain VC [auth a] MOL2 format, chain YA [auth F] MOL2 format, chain YC [auth a] MOL2 format, chain ZC [auth c] MOL2 format, chain WB [auth P] MOL2 format, chain WA [auth F] MOL2 format, chain TA [auth D] MOL2 format, chain RC [auth Z] MOL2 format, chain RA [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain IC [auth V] MOL2 format, chain GA [auth A] MOL2 format, chain BC [auth Q] mmCIF format, chain BB [auth G] mmCIF format, chain DB [auth I] mmCIF format, chain DC [auth U] mmCIF format, chain EB [auth J] mmCIF format, chain GB [auth K] mmCIF format, chain JC [auth V] mmCIF format, chain LB [auth L] mmCIF format, chain MB [auth L] mmCIF format, chain NB [auth L] mmCIF format, chain NC [auth X] mmCIF format, chain QA [auth D] mmCIF format, chain RB [auth N] mmCIF format, chain TB [auth N] mmCIF format, chain UC [auth a] mmCIF format, chain VC [auth a] mmCIF format, chain YA [auth F] mmCIF format, chain YC [auth a] mmCIF format, chain ZC [auth c] mmCIF format, chain WB [auth P] mmCIF format, chain WA [auth F] mmCIF format, chain TA [auth D] mmCIF format, chain RC [auth Z] mmCIF format, chain RA [auth D] mmCIF format, chain NA [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain IC [auth V] mmCIF format, chain GA [auth A] mmCIF format, chain BC [auth Q]	BB [auth G] BC [auth Q] DB [auth I] DC [auth U] EB [auth J] BB [auth G], BC [auth Q], DB [auth I], DC [auth U], EB [auth J], GA [auth A], GB [auth K], IC [auth V], JA [auth B], JC [auth V], LB [auth L], MB [auth L], NA [auth C], NB [auth L], NC [auth X], QA [auth D], RA [auth D], RB [auth N], RC [auth Z], TA [auth D], TB [auth N], UC [auth a], VC [auth a], WA [auth F], WB [auth P], YA [auth F], YC [auth a], ZC [auth c]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BB [auth G] Focus chain BC [auth Q] Focus chain DB [auth I] Focus chain DC [auth U] Focus chain EB [auth J] Focus chain GA [auth A] Focus chain GB [auth K] Focus chain IC [auth V] Focus chain JA [auth B] Focus chain JC [auth V] Focus chain LB [auth L] Focus chain MB [auth L] Focus chain NA [auth C] Focus chain NB [auth L] Focus chain NC [auth X] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain RB [auth N] Focus chain RC [auth Z] Focus chain TA [auth D] Focus chain TB [auth N] Focus chain UC [auth a] Focus chain VC [auth a] Focus chain WA [auth F] Focus chain WB [auth P] Focus chain YA [auth F] Focus chain YC [auth a] Focus chain ZC [auth c] Interactions & Density Focus chain BB [auth G] Focus chain BC [auth Q] Focus chain DB [auth I] Focus chain DC [auth U] Focus chain EB [auth J] Focus chain GA [auth A] Focus chain GB [auth K] Focus chain IC [auth V] Focus chain JA [auth B] Focus chain JC [auth V] Focus chain LB [auth L] Focus chain MB [auth L] Focus chain NA [auth C] Focus chain NB [auth L] Focus chain NC [auth X] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain RB [auth N] Focus chain RC [auth Z] Focus chain TA [auth D] Focus chain TB [auth N] Focus chain UC [auth a] Focus chain VC [auth a] Focus chain WA [auth F] Focus chain WB [auth P] Focus chain YA [auth F] Focus chain YC [auth a] Focus chain ZC [auth c]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.206 (Depositor), 0.203 (DCC)
R-Value Work: 0.171 (Depositor), 0.167 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.184	α = 90
b = 120.533	β = 95.36
c = 140.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Funding Organization	Location	Grant Number
China Scholarships Council	China	--
Royal Society	United Kingdom	RG130585

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-08-31
Changes: Database references
Version 1.2: 2018-01-31
Changes: Author supporting evidence
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-01-10
Changes: Refinement description