1JW8

1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF P6 FORM OF MYOGLOBIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments.

Kondrashov, D.A., Zhang, W., Aranda, R., Stec, B., Phillips Jr., G.N.

(2008) Proteins 70: 353-362

  • DOI: 10.1002/prot.21499
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a ra ...

    Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a range of crystallization conditions, often resulting in different space groups and changes in the packing arrangements. Three high resolution structures of myoglobin (Mb) in different crystal space groups are presented, including one in a new space group P6(1)22 and two structures in space groups P2(1)2(1)2(1) and P6. We compare coordinates and anisotropic displacement parameters (ADPs) from these three structures plus an existing structure in space group P2(1). While the overall changes are small, there is substantial variation in several external regions with varying patterns of crystal contacts across the space group packing arrangements. The structural ensemble containing four different crystal forms displays greater conformational variance (Calpha rmsd of 0.54-0.79 A) in comparison to a collection of four Mb structures with different ligands and mutations in the same crystal form (Calpha rmsd values of 0.28-0.37 A). The high resolution of the data enables comparison of both the magnitudes and directions of ADPs, which are found to be suppressed by crystal contacts. A composite dynamic profile of Mb structural variation from the four structures was compared with an independent structural ensemble developed from NMR refinement. Despite the limitations and biases of each method, the ADPs of the crystallographic ensemble closely match the positional variance from the solution NMR ensemble with linear correlation of 0.8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure.

    Organizational Affiliation: 

    Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
154Physeter catodonMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO
Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.380α = 90.00
b = 90.380β = 90.00
c = 45.340γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
MERLOTphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2001-09-03 
  • Released Date: 2001-10-10 
  • Deposition Author(s): Phillips Jr., G.N.

Revision History 

  • Version 1.0: 2001-10-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2013-01-30
    Type: Database references, Structure summary
  • Version 1.4: 2017-10-04
    Type: Refinement description