1UFP | pdb_00001ufp

Crystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me2-salophen)/apo-wild type Myoglobin

• PDB DOI: https://doi.org/10.2210/pdb1UFP/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-04 Released: 2004-05-18 
• Deposition Author(s): Ueno, T., Ohashi, M., Kono, M., Kondo, K., Suzuki, A., Yamane, T., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Artificial Metalloproteins: Tight Binding of Fe(III)(Schiff-Base) by Mutation of Ala71 to Gly in Apo-Myoglobin

Ueno, T., Ohashi, M., Kono, M., Kondo, K., Suzuki, A., Yamane, T., Watanabe, Y.

(2004) Inorg Chem 43: 2852-2858

• PubMed: 15106972 
• DOI: https://doi.org/10.1021/ic0498539
• Primary Citation Related Structures: 
  1UFJ, 1UFP


• PubMed Abstract: 
  

  Apo-myoglobin (apo-Mb) and apo-A71GMb were successfully reconstituted with FeIII(salophen) (1) (salophen = N,N'-bis(salicylidene)-1,2-phenilenediamine), Fe(III)(3,3'-Me2-salophen) (2), and FeIII(5,5'-t-Bu2-salophen) (3). The crystal structure of 2.apo-A71GMb shows the tight binding of the complex in the Mb cavity, while in wild-type apo-Mb it is highly disordered due to the steric repulsion with Ala71. Furthermore, the structure of 2.apo-A71GMb suggests a possible accommodation of a small substrate in the cavity. In fact, the cyanide association rate constant of 2.apo-A71GMb is 216-fold larger compared to that of 2.apo-Mb. These results provide us principles for the noncovalent fixation of synthetic metal cofactors at the desired positions in protein matrixes.

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Organizational Affiliation: 
• Research Center for Materials Science, Nagoya University, Nagoya 464-8602, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.94 kDa 
• Atom Count: 1,411 
• Modeled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.054	α = 90
b = 58.817	β = 90
c = 75.619	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Ueno, T., Ohashi, M., Kono, M., Kondo, K., Suzuki, A., Yamane, T., Watanabe, Y.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-08
  Changes: Data collection, Refinement description