7VP8 | pdb_00007vp8

Crystal structure of ferritin from Ureaplasma urealyticum

• PDB DOI: https://doi.org/10.2210/pdb7VP8/pdb

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


• Deposited: 2021-10-15 Released: 2022-08-24 
• Deposition Author(s): Wang, W., Liu, X., Wang, Y., Fu, D., Wang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: in silico

Literature

Distinct structural characteristics define a new subfamily of Mycoplasma ferritin

Wang, W., Liu, X., Wang, Y., Wang, Y., Fu, D., Xi, H., Zhao, Y., Wang, H.

(2022) Chin Chem Lett 33: 4952-4955

• DOI: https://doi.org/10.1016/j.cclet.2022.03.119

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.38 kDa 
• Atom Count: 1,635 
• Modeled Residue Count: 168 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin-like diiron domain-containing protein	A	172	Ureaplasma urealyticum	Mutation(s): 0  Gene Names: EPH05_02360

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A], C [auth A], D [auth A], E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.441	α = 90
b = 178.441	β = 90
c = 178.441	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Wang, W., Liu, X., Wang, Y., Fu, D., Wang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	62075118, 21601112

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description