3O89

Crystal Structure of Sperm Whale Myoglobin G65T

• PDB DOI: https://doi.org/10.2210/pdb3O89/pdb

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


• Deposited: 2010-08-02 Released: 2011-12-07 
• Deposition Author(s): Huang, X., Lovelace, L., Lebioda, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.183 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Investigations of Structural Factors that Influence the Mechanism of Halophenol Dehalogenation using 'Peroxidase-Like' Myoglobin mutants and 'Myoglobin-Like' Amphitrite ornata Dehaloperoxidase Mutants

Huang, X., Du, J., Dawson, J., Lebioda, L.

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)

Macromolecule Content

• Total Structure Weight: 18.09 kDa 
• Atom Count: 1,515 
• 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): 1  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
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.183 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.439	α = 90
b = 90.439	β = 90
c = 45.247	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Huang, X., Lovelace, L., Lebioda, L.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations