3ASE

Crystal Structure of Zinc myoglobin soaked with Ru3O cluster

• PDB DOI: https://doi.org/10.2210/pdb3ASE/pdb

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


• Deposited: 2010-12-11 Released: 2011-04-27 
• Deposition Author(s): Koshiyama, T., Shirai, M., Hikage, T., Tabe, H., Tanaka, K., Kitagawa, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Post-Crystal Engineering of Zinc-Substituted Myoglobin to Construct a Long-Lived Photoinduced Charge-Separation System

Koshiyama, T., Shirai, M., Hikage, T., Tabe, H., Tanaka, K., Kitagawa, S., Ueno, T.

(2011) Angew Chem Int Ed Engl 

• PubMed: 21495132 
• DOI: https://doi.org/10.1002/anie.201008004
• Primary Citation of Related Structures:  
  3ASE

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Organizational Affiliation: 

Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University iCeMS Lab Funai Center, Kyoto University Katsura, Kyoto 615-8510, Japan.

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: 18.82 kDa 
• Atom Count: 1,353 
• Modelled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	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
ZNH	F [auth A]	PROTOPORPHYRIN IX CONTAINING ZN C34 H32 N4 O4 Zn FUTVBRXUIKZACV-RGGAHWMASA-L
RUO	D [auth A], E [auth A]	oxo-centered triruthenium cluster O Ru3 VRRCAPVAMMGJAC-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.722	α = 90
b = 90.722	β = 90
c = 45.395	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Koshiyama, T., Shirai, M., Hikage, T., Tabe, H., Tanaka, K., Kitagawa, S., Ueno, T.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations