9IRE | pdb_00009ire

CRYSTAL STRUCTURE OF Bacillus cereus FERRIC UPTAKE REGULATOR

PDB DOI: https://doi.org/10.2210/pdb9IRE/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Bacillus cereus VD154
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-15 Released: 2025-07-23
Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, T.V., Kostareva, O.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.292 (Depositor), 0.291 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.217 (Depositor)

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

Literature

CRYSTAL STRUCTURE OF Bacillus cereus FERRIC UPTAKE REGULATOR

Gabdulkhakov, A.G., Tishchenko, T.V., Kostareva, O.S.

To be published.

Macromolecule Content

Total Structure Weight: 35.63 kDa
Atom Count: 2,424
Modeled Residue Count: 294
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric uptake regulation protein	A, B	151	Bacillus cereus VD154	Mutation(s): 0 Gene Names: IK5_03667
UniProt
Find proteins for A0A158RN89 (Bacillus cereus (strain 03BB102)) Explore A0A158RN89 Go to UniProtKB: A0A158RN89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A158RN89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.292 (Depositor), 0.291 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.009	α = 90
b = 99.009	β = 90
c = 61.253	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Gabdulkhakov, A.G.

Tishchenko, T.V.

Kostareva, O.S.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-07-23
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.