6KRF

An X-ray structure of ferric F43Y/F46S sperm whale myoglobin in complex with guaiacol

• PDB DOI: https://doi.org/10.2210/pdb6KRF/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter catodon
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2019-08-21 Released: 2020-07-01 
• Deposition Author(s): Yuan, H., Lin, Y.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

A Catalytic Binding Site Together with a Distal Tyr in MyoglobinAffords Catalytic Efficiencies Similar to Natural Peroxidases.

Zhang, P., Yuan, H., Xu, J., Wang, X.J., Gao, S.Q., Tan, X., Lin, Y.W.

(2020) ACS Catal 10: 891-896

• DOI: https://doi.org/10.1021/acscatal.9b05080

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: 17.93 kDa 
• Atom Count: 1,479 
• 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 catodon	Mutation(s): 2  Gene Names: MB
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
JZ3 (Subject of Investigation/LOI)	C [auth A]	Guaiacol C7 H8 O2 LHGVFZTZFXWLCP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.794	α = 90
b = 48.558	β = 90
c = 78.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Yuan, H., Lin, Y.W.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description