7XRG | pdb_00007xrg

ferritin nanocage assembly with nickel ion

• PDB DOI: https://doi.org/10.2210/pdb7XRG/pdb

• Classification: PROTEIN BINDING
• Organism(s): Penaeus japonicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-05-10 Released: 2023-05-17 
• Deposition Author(s): Zhao, G.H., Zhang, X.R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

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

Starting Model: experimental

Literature

ferritin nanocage assembly with nickel ion

Zhao, G.H., Zhang, X.R.

To be published.

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: 19.81 kDa 
• Atom Count: 1,488 
• Modeled Residue Count: 169 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A	170	Penaeus japonicus	Mutation(s): 4  EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus) Explore T2B7E1  Go to UniProtKB:  T2B7E1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI (Subject of Investigation/LOI)	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FE	D [auth A], E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.278	α = 90
b = 117.278	β = 90
c = 117.278	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Zhao, G.H., Zhang, X.R.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31972018

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection
• Version 1.2: 2023-11-29
  Changes: Refinement description