4FWY

F33Y CuB myoglobin (F33Y L29H F43H sperm whale myoglobin) with copper bound

• PDB DOI: https://doi.org/10.2210/pdb4FWY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-07-02 Released: 2012-07-18 
• Deposition Author(s): Gao, Y.-G., Robinson, H., Petrik, I.D., Miner, K.D., Lu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

A Designed Functional Metalloenzyme that Reduces O(2) to H(2) O with Over One Thousand Turnovers.

Miner, K.D., Mukherjee, A., Gao, Y.G., Null, E.L., Petrik, I.D., Zhao, X., Yeung, N., Robinson, H., Lu, Y.

(2012) Angew Chem Int Ed Engl 51: 5589-5592

• PubMed: 22539151 
• DOI: https://doi.org/10.1002/anie.201201981
• Primary Citation of Related Structures:  
  4FWX, 4FWY, 4FWZ


• PubMed Abstract: 
  

  [Image: see text] Rational design of functional enzymes with high turnovers is a significant challenge, especially those with complex active site and difficult reactions, such as in respiratory oxidases. Introducing 2 His and 1 Tyr into myoglobin resulted in designed enzymes that reduce O ₂ to H ₂ O with > 1000 turnovers and minimal release of reactive oxygen species. This also showed that presence and positioning of Tyr, not Cu, are critical for activity.

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Organizational Affiliation: 

Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 18.2 kDa 
• Atom Count: 1,316 
• Modelled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 3  Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CU	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.734	α = 90
b = 48.286	β = 90
c = 77.691	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Gao, Y.-G., Robinson, H., Petrik, I.D., Miner, K.D., Lu, Y.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description