8X3H | pdb_00008x3h

Crystal structure of iron-bound recombinant ovotransferrin N-lobe at 0.93 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb8X3H/pdb

• Classification: METAL TRANSPORT
• Organism(s): Gallus gallus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-11-13 Released: 2023-12-13 
• Deposition Author(s): Toyoda, M., Mikami, B., Mizutani, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.93 Å
• R-Value Free: 
  0.124 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.103 (Depositor), 0.110 (DCC) 

Starting Model: experimental

Literature

Crystal structure of iron-bound ovotransferrin N-lobe at atomic resolution

Toyoda, M., Tanabe, A., Mikami, B., Hirose, M., Mizutani, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.74 kDa 
• Atom Count: 3,494 
• Modeled Residue Count: 332 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ovotransferrin	A	332	Gallus gallus	Mutation(s): 0  Gene Names: TFEW
UniProt
Find proteins for P02789 (Gallus gallus) Explore P02789  Go to UniProtKB:  P02789

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3 (Subject of Investigation/LOI)	C [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.93 Å
• R-Value Free:  0.124 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.103 (Depositor), 0.110 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.346	α = 90
b = 75.518	β = 90
c = 84.647	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Toyoda, M., Mikami, B., Mizutani, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary