9D8D | pdb_00009d8d

Crystal structure of Vibrio cholerae NFeoB in the GMPPCP-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

The Structure of the Full Catalytic Cycle of Vibrio cholerae NFeoB.

Magante, K.Armstrong, C.M.Lee, M.Smith, A.T.

(2026) J Mol Biology 438: 169727-169727

  • DOI: https://doi.org/10.1016/j.jmb.2026.169727
  • Primary Citation of Related Structures:  
    9D8B, 9D8D

  • PubMed Abstract: 

    The acquisition of iron is critical for the survival and the virulence of numerous infectious pathogens, and most bacteria acquire ferrous iron (Fe 2+ ) by utilizing the ferrous iron transport (Feo) system. FeoB is the main component of this system and its function is regulated by its soluble cytosolic domain, termed NFeoB. We have recently begun to define the structure and the mechanism of the Feo system from the bacterium Vibrio cholerae, the causative agent of the disease cholera. However, major structural gaps in our understanding of the nucleotide-promiscuous V. cholerae NFeoB still exist. In this work, we have determined several new X-ray crystal structures that reveal distinct snapshots of the VcNFeoB domain in uncommon and unprecedented states, ultimately illuminating the full catalytic cycle of this NTPase. This work reveals important functional features of VcNFeoB that may be leveraged and ultimately targeted to prevent the infectivity and the spread of cholera.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferrous iron transport protein B
A, B, C, D
261Vibrio choleraeMutation(s): 0 
Gene Names: feoB_1ERS013165_00117
UniProt
Find proteins for A0A0X1KYD0 (Vibrio cholerae (strain MO10))
Explore A0A0X1KYD0 
Go to UniProtKB:  A0A0X1KYD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0X1KYD0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth C],
J [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth C],
K [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.977α = 93.59
b = 59.666β = 92.61
c = 89.432γ = 113.77
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133497
National Science Foundation (NSF, United States)United StatesCHE1844624

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 2.0: 2026-01-14
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2026-03-18
    Changes: Database references