5ZZE | pdb_00005zze

Crystal structure of horse myoglobin crystallized by ammonium sulfate

• PDB DOI: https://doi.org/10.2210/pdb5ZZE/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2018-06-01 Released: 2019-02-20 
• Deposition Author(s): Kitahara, M., Fudo, S., Yoneda, T., Nukaga, M., Hoshino, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Anisotropic Distribution of Ammonium Sulfate Ions in Protein Crystallization

Kitahara, M., Fudo, S., Yoneda, T., Nukaga, M., Hoshino, T.

(2019) Cryst Growth Des 19: 6004-6010

• DOI: https://doi.org/10.1021/acs.cgd.9b00256

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: 17.83 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	152	Equus caballus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P68082 (Equus caballus) Explore P68082  Go to UniProtKB:  P68082

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], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.264	α = 90
b = 28.588	β = 105.75
c = 62.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Kitahara, M., Fudo, S., Yoneda, T., Nukaga, M., Hoshino, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	15K08458

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references