Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17885.41 
• Atom Count: 1418 
• Residue Count: 151 
• Unique protein chains: 1

1A6G

CARBONMONOXY-MYOGLOBIN, ATOMIC RESOLUTION

• DOI: 10.2210/pdb1A6G/pdb

• Classification: HEME PROTEIN
• Organism(s): Physeter catodon


• Deposited: 1998-02-25 Released: 1998-10-21 
• Deposition Author(s): Vojtechovsky, J., Chu, K., Berendzen, J., Sweet, R.M., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.160 

Literature

Crystal structures of myoglobin-ligand complexes at near-atomic resolution.

Vojtechovsky, J., Chu, K., Berendzen, J., Sweet, R.M., Schlichting, I.

(1999) Biophys.J. 77: 2153-2174

• PubMed: 10512835 
• DOI: 10.1016/S0006-3495(99)77056-6
• Primary Citation of Related Structures:  
  1A6N, 1A6M, 1A6K


• PubMed Abstract: 
  

We have used x-ray crystallography to determine the structures of sperm whale myoglobin (Mb) in four different ligation states (unligated, ferric aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better than 1.2 A. Data collection and analysis were performed in as much the same way as possible to reduce model bias in differences between structures. The structural differences among the ligation states are much smaller than previously estimated, with differences of <0.25 A root-mean-square deviation among all atoms. One structural parameter previously thought to vary among the ligation states, the proximal histidine (His-93) azimuthal angle, is nearly identical in all the ferrous complexes, although the tilt of the proximal histidine is different in the unligated form. There are significant differences, however, in the heme geometry, in the position of the heme in the pocket, and in the distal histidine (His-64) conformations. In the CO complex the majority conformation of ligand is at an angle of 18 +/- 3 degrees with respect to the heme plane, with a geometry similar to that seen in encumbered model compounds; this angle is significantly smaller than reported previously by crystallographic studies on monoclinic Mb crystals, but still significantly larger than observed by photoselection. The distal histidine in unligated Mb and in the dioxygenated complex is best described as having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in low-pH structures where His-64 is doubly protonated. We suggest that these conformations of the distal histidine correspond to the different conformational substates of MbCO and MbO(2) seen in vibrational spectra. Full-matrix refinement provides uncertainty estimates of important structural parameters. Anisotropic refinement yields information about correlated disorder of atoms; we find that the proximal (F) helix and heme move approximately as rigid bodies, but that the distal (E) helix does not.

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Organizational Affiliation: 

Max Planck Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, 44227 Dortmund, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MYOGLOBIN	A	151	Physeter catodon	Mutation(s): 0  Gene Names: MB
Find proteins for P02185 (Physeter catodon) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 63.800	α = 90.00
b = 30.630	β = 105.80
c = 34.420	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXL-97	refinement
SHELXL-97	phasing
SHELXL-97	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-25 
• Released Date: 1998-10-21 
• Deposition Author(s): Vojtechovsky, J., Chu, K., Berendzen, J., Sweet, R.M., Schlichting, I.

Revision History 

• Version 1.0: 1998-10-21
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance