9D8D | pdb_00009d8d

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

PDB DOI: https://doi.org/10.2210/pdb9D8D/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-19 Released: 2025-09-03
Deposition Author(s): Lee, M., Magante, K.D., Smith, A.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

Lee, M., Magante, K.D., Smith, A.T.

To be published.

Macromolecule Content

Total Structure Weight: 119.11 kDa
Atom Count: 8,194
Modeled Residue Count: 997
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferrous iron transport protein B	A, B, C, D	260	Vibrio cholerae	Mutation(s): 0 Gene Names: feoB_1, ERS013165_00117
UniProt
Find proteins for A0A0X1KYD0 (Vibrio cholerae (strain MO10)) Explore A0A0X1KYD0 Go to UniProtKB: A0A0X1KYD0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0X1KYD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP Query on GCP Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], J [auth D]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]

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 = 53.977	α = 93.59
b = 59.666	β = 92.61
c = 89.432	γ = 113.77

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Lee, M.

Magante, K.D.

Smith, A.T.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133497
National Science Foundation (NSF, United States)	United States	CHE1844624