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: 18035.63 
• Atom Count: 1270 
• Residue Count: 154 
• Unique protein chains: 1

1CIK

RECOMBINANT SPERM WHALE MYOGLOBIN I99A MUTANT (MET)

• DOI: 10.2210/pdb1CIK/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Physeter catodon
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 1999-04-01 Released: 1999-04-09 
• Deposition Author(s): Liong, E.C., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.193 

Literature

Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin.

Liong, E.C., Dou, Y., Scott, E.E., Olson, J.S., Phillips Jr., G.N.

(2001) J.Biol.Chem. 276: 9093-9100

• PubMed: 11084036 
• DOI: 10.1074/jbc.M008593200
• Primary Citation of Related Structures:  
  1DTI, 1CPW, 1CP5, 1CP0, 1CO9, 1CO8, 1CIO, 1CH9, 1CH7, 1CH5, 1CH3, 1CH2, 1CH1


• PubMed Abstract: 
  

The ability of myoglobin to bind oxygen reversibly depends critically on retention of the heme prosthetic group. Globin side chains at the Leu(89)(F4), His(97)(FG3), Ile(99)(FG5), and Leu(104)(G5) positions on the proximal side of the heme pocket strongly influence heme affinity. The roles of these amino acids in preventing heme loss have been examined by determining high resolution structures of 14 different mutants at these positions using x-ray crystallography. Leu(89) and His(97) are important surface amino acids that interact either sterically or electrostatically with the edges of the porphyrin ring. Ile(99) and Leu(104) are located in the interior region of the proximal pocket beneath ring C of the heme prosthetic group. The apolar amino acids Leu(89), Ile(99), and Leu(104) "waterproof" the heme pocket by forming a barrier to solvent penetration, minimizing the size of the proximal cavity, and maintaining a hydrophobic environment. Substitutions with smaller or polar side chains at these positions result in exposure of the heme to solvent, the appearance of crystallographically defined water molecules in or near the proximal pocket, and large increases in the rate of hemin loss. Thus, the naturally occurring amino acid side chains at these positions serve to prevent hydration of the His(93)-Fe(III) bond and are highly conserved in all known myoglobins and hemoglobins.

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Organizational Affiliation: 

Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (MYOGLOBIN)	A	154	Physeter catodon	Mutation(s): 2  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: 0.193 
• Space Group: P 6

Unit Cell:

Length (Å)	Angle (°)
a = 91.497	α = 90.00
b = 91.497	β = 90.00
c = 45.944	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHELXS	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-01 
• Released Date: 1999-04-09 
• Deposition Author(s): Liong, E.C., Phillips Jr., G.N.

Revision History 

• Version 1.0: 1999-04-09
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance