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

Validation slider image for 9FJ2

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	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 DA [auth F] SDF format, chain HA [auth G] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth D]	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]

Experimental Data & Validation

Experimental Data

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)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.767	α = 93.29
b = 67.674	β = 98.337
c = 95.325	γ = 106.878

Software Package:

Software Name	Purpose
autoPROC	data processing
PHENIX	refinement
Aimless	data scaling
MoRDa	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Salgueiro, B.A.

Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	--

Revision History (Full details and data files)

Version 1.0: 2025-06-11
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.