7W8F | pdb_00007w8f

Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal

• PDB DOI: https://doi.org/10.2210/pdb7W8F/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-07 Released: 2022-12-07 
• Deposition Author(s): Tomoo, K., Miyamoto, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal

Tomoo, K., Miyamoto, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 31.82 kDa 
• Atom Count: 2,376 
• Modeled Residue Count: 278 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative periplasm binding protein	A	280	Vibrio vulnificus	Mutation(s): 0  Gene Names: fhuD
UniProt
Find proteins for Q845T3 (Vibrio vulnificus) Explore Q845T3  Go to UniProtKB:  Q845T3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KTY (Subject of Investigation/LOI)	B [auth A]	desferrioxamine B C25 H48 N6 O8 UBQYURCVBFRUQT-UHFFFAOYSA-N
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.8	α = 90
b = 57.89	β = 95.02
c = 62.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Tomoo, K., Miyamoto, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description