Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18235.69 
• Atom Count: 1266 
• Residue Count: 153 
• Unique protein chains: 1

1JPB

Sperm Whale met-Myoglobin (low temperature; high pressure)

• DOI: 10.2210/pdb1JPB/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter catodon


• Deposited: 2001-08-01 Released: 2002-01-16 
• Deposition Author(s): Urayama, P., Gruner, S.M., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.237 
• R-Value Work: 0.209 

Literature

Probing substates in sperm whale myoglobin using high-pressure crystallography.

Urayama, P., Phillips Jr., G.N., Gruner, S.M.

(2002) Structure 10: 51-60

• PubMed: 11796110 
• Primary Citation of Related Structures:  
  1JP9, 1JP8, 1JP6


• PubMed Abstract: 
  

Pressures in the 100 MPa range are known to have an enormous number of effects on the action of proteins, but straightforward means for determining the structural basis of these effects have been lacking. Here, crystallography has been used to probe effects of pressure on sperm whale myoglobin structure. A comparison of pressure effects with those seen at low pH suggests that structural changes under pressure are interpretable as a shift in the populations of conformational substates. Furthermore, a novel high-pressure protein crystal-cooling method has been used to show low-temperature metastability, providing an alternative to room temperature, beryllium pressure cell-based techniques. The change in protein structure due to pressure is not purely compressive and involves conformational changes important to protein activity. Correlation with low-pH structures suggests observed structural changes are associated with global conformational substates. Methods developed here open up a direct avenue for exploration of the effects of pressure on proteins.

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Organizational Affiliation: 

Department of Physics, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
myoglobin	A	153	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 2 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.237 
• R-Value Work: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 63.800	α = 90.00
b = 30.700	β = 105.61
c = 34.390	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
CNS	refinement
DPS	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-01 
• Released Date: 2002-01-16 
• Deposition Author(s): Urayama, P., Gruner, S.M., Phillips Jr., G.N.

Revision History 

• Version 1.0: 2002-01-16
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance