1BZ6

ATOMIC RESOLUTION CRYSTAL STRUCTURE AQUOMET-MYOGLOBIN FROM SPERM WHALE AT ROOM TEMPERATURE

• PDB DOI: https://doi.org/10.2210/pdb1BZ6/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter catodon
• Mutation(s): No 


• Deposited: 1998-11-05 Released: 1999-05-10 
• Deposition Author(s): Popov, A.N., Kachalova, G.S., Bartunik, H.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Observed: 0.091 

Starting Model: experimental

Literature

A steric mechanism for inhibition of CO binding to heme proteins.

Kachalova, G.S., Popov, A.N., Bartunik, H.D.

(1999) Science 284: 473-476

• PubMed: 10205052 
• DOI: https://doi.org/10.1126/science.284.5413.473
• Primary Citation of Related Structures:  
  1BZ6, 1BZP, 1BZR


• PubMed Abstract: 
  

  The crystal structures of myoglobin in the deoxy- and carbon monoxide-ligated states at a resolution of 1.15 angstroms show that carbon monoxide binding at ambient temperatures requires concerted motions of the heme, the iron, and helices E and F for relief of steric inhibition. These steps constitute the main mechanism by which heme proteins lower the affinity of the heme group for the toxic ligand carbon monoxide.

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Organizational Affiliation: 

Max-Planck-Arbeitsgruppen für Strukturelle Molekularbiologie, Arbeitsgruppe Proteindynamik, Notkestrabetae 85, 22603 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.24 kDa 
• Atom Count: 1,691 
• Modelled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MYOGLOBIN)	A	153	Physeter catodon	Mutation(s): 0  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	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A], 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: 1.20 Å
• R-Value Observed: 0.091 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.83	α = 90
b = 30.92	β = 105.5
c = 64.57	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-10 
Deposition Author(s): Popov, A.N., Kachalova, G.S., Bartunik, H.D.

Revision History  

• Version 1.0: 1999-05-10
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description