5IKS

Wild-type sperm whale myoglobin with a Fe-phenyl moiety

• PDB DOI: https://doi.org/10.2210/pdb5IKS/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Physeter catodon
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-03 Released: 2016-09-21 
• Deposition Author(s): Wang, B., Thomas, L.M., Richter-Addo, G.B.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.278 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations.

Wang, B., Thomas, L.M., Richter-Addo, G.B.

(2016) J Inorg Biochem 164: 1-4

• PubMed: 27687333 
• DOI: https://doi.org/10.1016/j.jinorgbio.2016.06.028
• Primary Citation of Related Structures:  
  5IKS, 5ILE, 5ILM, 5ILP, 5ILR


• PubMed Abstract: 
  

  Bioorganometallic Fe-C bonds are biologically relevant species that may result from the metabolism of natural or synthetic hydrazines. The molecular structures of four new sperm whale mutant myoglobin derivatives with Fe-aryl moieties, namely H64A-tolyl-m, H64A-chlorophenyl-p, H64Q-tolyl-m, and H64Q-chlorophenyl-p, have been determined at 1.7-1.9Å resolution. The structures reveal conformational preferences for the substituted aryls resulting from attachment of the aryl ligands to Fe at the site of net -NHNH ₂ release from the precursor hydrazines, and show distal pocket changes that readily accommodate these bulky ligands.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, and Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman 73019, United States.

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: 17.93 kDa 
• Atom Count: 1,329 
• Modelled Residue Count: 151 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	151	Physeter catodon	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6CO	B [auth A]	[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)di(propanoato)(2-)](phenyl)iron C40 H37 Fe N4 O4 JQRFCQNWEWEPHL-HXFTUNQESA-L
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.278 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.484	α = 90
b = 30.152	β = 105.16
c = 64.463	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Wang, B., Thomas, L.M., Richter-Addo, G.B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 1213674

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2016-12-28
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description