6K4M

Cryo-EM structure of Holo-bacterioferritin form-II from Streptomyces coelicolor

PDB DOI: https://doi.org/10.2210/pdb6K4M/pdb
EM Map EMD-9915: EMDB EMDataResource

Classification: METAL TRANSPORT
Organism(s): Streptomyces coelicolor
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-05-24 Released: 2021-02-03
Deposition Author(s): Jobichen, C., Sivaraman, J.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of Bacterioferritin from Streptomyces coelicolor

Jobichen, C., Sivaraman, J.

To be published.

Macromolecule Content

Total Structure Weight: 470.56 kDa
Atom Count: 31,508
Modelled Residue Count: 3,790
Deposited Residue Count: 4,008
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A B C D E [auth F] A, B, C, D, E [auth F], F [auth E], G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	167	Streptomyces coelicolor	Mutation(s): 0 EC: 1.16.3.1
UniProt
Find proteins for Q9S2N0 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9S2N0 Go to UniProtKB: Q9S2N0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9S2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain CB [auth U] SDF format, chain FA [auth F] SDF format, chain FB [auth W] SDF format, chain GB [auth X] SDF format, chain JA [auth H] SDF format, chain MA [auth K] SDF format, chain PA [auth L] SDF format, chain UA [auth P] SDF format, chain WA [auth R] SDF format, chain Z [auth A] SDF format, chain ZA [auth S] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth U] MOL2 format, chain FA [auth F] MOL2 format, chain FB [auth W] MOL2 format, chain GB [auth X] MOL2 format, chain JA [auth H] MOL2 format, chain MA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain UA [auth P] MOL2 format, chain WA [auth R] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth S] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth U] mmCIF format, chain FA [auth F] mmCIF format, chain FB [auth W] mmCIF format, chain GB [auth X] mmCIF format, chain JA [auth H] mmCIF format, chain MA [auth K] mmCIF format, chain PA [auth L] mmCIF format, chain UA [auth P] mmCIF format, chain WA [auth R] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth S]	CA [auth C] CB [auth U] FA [auth F] FB [auth W] GB [auth X] CA [auth C], CB [auth U], FA [auth F], FB [auth W], GB [auth X], JA [auth H], MA [auth K], PA [auth L], UA [auth P], WA [auth R], Z [auth A], ZA [auth S]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CA [auth C] Focus chain CB [auth U] Focus chain FA [auth F] Focus chain FB [auth W] Focus chain GB [auth X] Focus chain JA [auth H] Focus chain MA [auth K] Focus chain PA [auth L] Focus chain UA [auth P] Focus chain WA [auth R] Focus chain Z [auth A] Focus chain ZA [auth S] Interactions & Density Focus chain CA [auth C] Focus chain CB [auth U] Focus chain FA [auth F] Focus chain FB [auth W] Focus chain GB [auth X] Focus chain JA [auth H] Focus chain MA [auth K] Focus chain PA [auth L] Focus chain UA [auth P] Focus chain WA [auth R] Focus chain Z [auth A] Focus chain ZA [auth S]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth T] SDF format, chain BA [auth C] SDF format, chain BB [auth U] SDF format, chain DA [auth D] SDF format, chain DB [auth V] SDF format, chain EA [auth F] SDF format, chain EB [auth W] SDF format, chain GA [auth E] SDF format, chain HA [auth G] SDF format, chain HB [auth X] SDF format, chain IA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain OA [auth L] SDF format, chain QA [auth M] SDF format, chain RA [auth N] SDF format, chain SA [auth O] SDF format, chain TA [auth P] SDF format, chain VA [auth Q] SDF format, chain XA [auth R] SDF format, chain Y [auth A] SDF format, chain YA [auth S] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth T] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth U] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth V] MOL2 format, chain EA [auth F] MOL2 format, chain EB [auth W] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth G] MOL2 format, chain HB [auth X] MOL2 format, chain IA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain RA [auth N] MOL2 format, chain SA [auth O] MOL2 format, chain TA [auth P] MOL2 format, chain VA [auth Q] MOL2 format, chain XA [auth R] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth S] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth T] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth U] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth V] mmCIF format, chain EA [auth F] mmCIF format, chain EB [auth W] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth G] mmCIF format, chain HB [auth X] mmCIF format, chain IA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain OA [auth L] mmCIF format, chain QA [auth M] mmCIF format, chain RA [auth N] mmCIF format, chain SA [auth O] mmCIF format, chain TA [auth P] mmCIF format, chain VA [auth Q] mmCIF format, chain XA [auth R] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth S]	AA [auth B] AB [auth T] BA [auth C] BB [auth U] DA [auth D] AA [auth B], AB [auth T], BA [auth C], BB [auth U], DA [auth D], DB [auth V], EA [auth F], EB [auth W], GA [auth E], HA [auth G], HB [auth X], IA [auth H], KA [auth I], LA [auth J], NA [auth K], OA [auth L], QA [auth M], RA [auth N], SA [auth O], TA [auth P], VA [auth Q], XA [auth R], Y [auth A], YA [auth S]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth T] Focus chain BA [auth C] Focus chain BB [auth U] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain EA [auth F] Focus chain EB [auth W] Focus chain GA [auth E] Focus chain HA [auth G] Focus chain HB [auth X] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth O] Focus chain TA [auth P] Focus chain VA [auth Q] Focus chain XA [auth R] Focus chain Y [auth A] Focus chain YA [auth S] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth T] Focus chain BA [auth C] Focus chain BB [auth U] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain EA [auth F] Focus chain EB [auth W] Focus chain GA [auth E] Focus chain HA [auth G] Focus chain HB [auth X] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth O] Focus chain TA [auth P] Focus chain VA [auth Q] Focus chain XA [auth R] Focus chain Y [auth A] Focus chain YA [auth S]