5ZEO | pdb_00005zeo

X-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant with an intramolecular disulfide bond

• PDB DOI: https://doi.org/10.2210/pdb5ZEO/pdb

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


• Deposited: 2018-02-27 Released: 2018-05-09 
• Deposition Author(s): Yuan, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.266 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.223 (DCC) 

Starting Model: experimental

Literature

Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin

Yin, L.L., Yuan, H., Du, K.J., He, B., Gao, S.Q., Wen, G.B., Tan, X., Lin, Y.W.

(2018) Chem Commun (Camb) 54: 4356-4359

• PubMed: 29645029 
• DOI: https://doi.org/10.1039/c8cc01646a
• Primary Citation Related Structures: 
  5ZEO


• PubMed Abstract: 
  

  A de novo designed intramolecular disulfide bond in myoglobin, resembling that in cytoglobin without structural evidence, was confirmed by an X-ray structure for the first time and was demonstrated to regulate both the structure and function of this protein, which fulfills the design of an artificial dehaloperoxidase, with an activity exceeding that of a native enzyme.

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Organizational Affiliation: 
• School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. [e-mail] [e-mail].

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: 17.8 kDa 
• Atom Count: 1,428 
• Modeled 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 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.266 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.223 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.566	α = 90
b = 47.351	β = 90
c = 79.111	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Yuan, H.

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary