5GGX | pdb_00005ggx

Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb5GGX/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-16 Released: 2017-02-22
Deposition Author(s): Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.
Funding Organization(s): DAE(BRNS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.236 (Depositor), 0.247 (DCC)
R-Value Work:
0.200 (Depositor), 0.216 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae

Agarwal, S., Biswas, M., Dasgupta, J.

To be published.

Macromolecule Content

Total Structure Weight: 127.72 kDa
Atom Count: 8,438
Modeled Residue Count: 1,064
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron(III) ABC transporter, periplasmic iron-compound-binding protein	A, B, C, D	282	Vibrio cholerae O395	Mutation(s): 0 Gene Names: VC0395_A2582
UniProt
Find proteins for A0A0H3AJ03 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AJ03 Go to UniProtKB: A0A0H3AJ03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3AJ03
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DEF Query on DEF Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	DEFEROXAMINE MESYLATE FE(III) COMPLEX C₂₇ H₄₉ Fe N₆ O₁₁ S UZNCKXZKODNQDS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.236 (Depositor), 0.247 (DCC)
R-Value Work: 0.200 (Depositor), 0.216 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.145	α = 90
b = 191.145	β = 90
c = 129.164	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
SCALA	data scaling
PHASER	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Funding Organization	Location	Grant Number
DAE(BRNS)	India	--

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.