7V4V | pdb_00007v4v

polylysine induce assembly of Thermotoga maritima ferritin

• PDB DOI: https://doi.org/10.2210/pdb7V4V/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-15 Released: 2022-09-28 
• Deposition Author(s): Zhang, X., Zhao, G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

polylysine induce assembly of Thermotoga maritima ferritin

Zhang, X., Zhao, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.05 kDa 
• Atom Count: 5,557 
• Modeled Residue Count: 651 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A [auth H], B [auth A], C [auth B], D [auth C]	164	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1128 EC: 1.16.3.2
UniProt
Find proteins for Q9X0L2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0L2  Go to UniProtKB:  Q9X0L2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	E [auth H], F [auth H], G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.808	α = 90
b = 94.495	β = 90
c = 108.121	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Zhang, X., Zhao, G.

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

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description