6LRU | pdb_00006lru

Marsupenaeus japonicus ferritin mutant (T158H)

• PDB DOI: https://doi.org/10.2210/pdb6LRU/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Penaeus japonicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-01-16 Released: 2020-11-25 
• Deposition Author(s): Zhao, G., Tan, X., Zhang, T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Converting histidine-induced 3D protein arrays in crystals into their 3D analogues in solution by metal coordination cross-linking.

Tan, X., Chen, H., Gu, C., Zhang, J., Zhang, T., Wang, H., Zhao, G.

(2020) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-020-00394-x

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: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 19.84 kDa 
• Atom Count: 1,576 
• 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): 1  EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus) Explore T2B7E1  Go to UniProtKB:  T2B7E1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	B [auth A], F [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
NI (Subject of Investigation/LOI)	D [auth A], E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.349	α = 90
b = 117.349	β = 90
c = 117.349	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Zhao, G., Tan, X., Zhang, T.

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

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description