9FJ2 | pdb_00009fj2

Rubrerythrin from Clostridium difficile P28

PDB DOI: https://doi.org/10.2210/pdb9FJ2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridioides difficile P28
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-05-30 Released: 2025-06-11
Deposition Author(s): Salgueiro, B.A., Matias, P.M., Romao, C.V.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.321 (Depositor), 0.320 (DCC)
R-Value Work:
0.264 (Depositor), 0.264 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The X-ray crystal structure of the Rubrerythrin from Clostridium difficile P28 obtain by microdialysis method.

Salgueiro, B.A., Matias, P.M., Romao, C.V.

To be published.

Macromolecule Content

Total Structure Weight: 164.83 kDa
Atom Count: 11,797
Modeled Residue Count: 1,405
Deposited Residue Count: 1,424
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubrerythrin	A, B, C, D, E A, B, C, D, E, F, G, H	178	Clostridioides difficile P28	Mutation(s): 0 Gene Names: CIAN88_10840, DXA38_08075, G4D54_07625, I5Q87_04165
UniProt
Find proteins for A0A099I6D2 (Clostridium innocuum) Explore A0A099I6D2 Go to UniProtKB: A0A099I6D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A099I6D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain V [auth D] SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain KA [auth H] SDF format, chain K [auth A] SDF format, chain JA [auth H] SDF format, chain J [auth A] SDF format, chain IA [auth H] SDF format, chain I [auth A] SDF format, chain GA [auth G] SDF format, chain EA [auth G] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain KA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain KA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth F] EA [auth G] FA [auth G] AA [auth F], BA [auth F], CA [auth F], EA [auth G], FA [auth G], GA [auth G], I [auth A], IA [auth H], J [auth A], JA [auth H], K [auth A], KA [auth H], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth D], U [auth D], V [auth D], X [auth E], Y [auth E], Z [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
O (Subject of Investigation/LOI) Query on O Download Ideal Coordinates CCD File SDF format, chain HA [auth G] SDF format, chain P [auth B] SDF format, chain W [auth D] SDF format, chain L [auth A] SDF format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain W [auth D] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth F]	DA [auth F], HA [auth G], L [auth A], P [auth B], W [auth D]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain L [auth A] Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain L [auth A] Focus chain P [auth B] Focus chain W [auth D]