3QM9 | pdb_00003qm9

Blackfin tuna azido-myoglobin, atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb3QM9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thunnus atlanticus
• Mutation(s): No 


• Deposited: 2011-02-03 Released: 2012-02-08 
• Deposition Author(s): de Serrano, V.S., Rodriguez, M.M., Schreiter, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.91 Å
• R-Value Free: 
  0.133 (Depositor), 0.134 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.122 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

High Resolution Structures of Blackfin Tuna Myoglobin

de Serrano, V.S., Rodriguez, M.M., Schreiter, E.R.

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: 16.51 kDa 
• Atom Count: 1,665 
• Modeled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	146	Thunnus atlanticus	Mutation(s): 0
UniProt
Find proteins for H3JQV6 (Thunnus atlanticus) Explore H3JQV6  Go to UniProtKB:  H3JQV6

Small Molecules

Ligands 3 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
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI	C [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.91 Å
• R-Value Free:  0.133 (Depositor), 0.134 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.122 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.008	α = 90
b = 51.894	β = 103.95
c = 38.644	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): de Serrano, V.S., Rodriguez, M.M., Schreiter, E.R.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary