5ZZG

X-ray structure of F43Y/H64D sperm whale myoglobin in complex with TCP

• PDB DOI: https://doi.org/10.2210/pdb5ZZG/pdb

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


• Deposited: 2018-06-01 Released: 2018-10-03 
• Deposition Author(s): Yuan, H., Lin, Y.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase

Yin, L.L., Yuan, H., Liu, C., He, B., Gao, S.Q., Wen, G.B., Tan, X., Lin, Y.W.

(2018) ACS Catal 8: 9619-9624

• DOI: https://doi.org/10.1021/acscatal.8b02979

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: 18.04 kDa 
• Atom Count: 1,425 
• 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 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
T6C	C [auth A]	2,4,6-trichlorophenol C6 H3 Cl3 O LINPIYWFGCPVIE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.899	α = 90
b = 49.477	β = 90
c = 77.333	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Yuan, H., Lin, Y.W.

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description