7DLB | pdb_00007dlb

Crassostrea gigas ferritin mutant-D119K

• PDB DOI: https://doi.org/10.2210/pdb7DLB/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Magallana gigas
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-11-26 Released: 2021-12-01 
• Deposition Author(s): Li, H., Zang, J., Wang, Z., Du, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crassostrea gigas ferritin mutant-D119K

Li, H., Zang, J., Wang, Z., Du, M.

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: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 40.13 kDa 
• Atom Count: 2,899 
• Modeled Residue Count: 338 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B	171	Magallana gigas	Mutation(s): 1  Gene Names: fer, CGI_10027591 EC: 1.16.3.1
UniProt
Find proteins for Q70MM3 (Magallana gigas) Explore Q70MM3  Go to UniProtKB:  Q70MM3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.702	α = 90
b = 150.702	β = 90
c = 150.702	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Li, H., Zang, J., Wang, Z., Du, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31730069

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description