9GZU | pdb_00009gzu

Crystal structure of apo-bacterioferritin (Bfr) from Brucella melitentsis

PDB DOI: https://doi.org/10.2210/pdb9GZU/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Brucella melitensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-04 Released: 2025-10-15
Deposition Author(s): Scaillet, T., Champagne, C., Wouters, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of apo-bacterioferritin (Bfr) from Brucella melitentsis

Scaillet, T., Clement, C., Wouters, J.

To be published.

Macromolecule Content

Total Structure Weight: 19.28 kDa
Atom Count: 1,515
Modeled Residue Count: 162
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A	165	Brucella melitensis	Mutation(s): 0 Gene Names: bfr, BruAb2_0659 EC: 1.16.3.1
UniProt
Find proteins for F8WJU0 (Brucella abortus biovar 1 (strain 9-941)) Explore F8WJU0 Go to UniProtKB: F8WJU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8WJU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain B [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	B [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.78	α = 90
b = 173.78	β = 90
c = 173.78	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-15
Type: Initial release

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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.