1DM1 | pdb_00001dm1

2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF MYOGLOBIN FROM APLYSIA LIMACINA

• PDB DOI: https://doi.org/10.2210/pdb1DM1/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Aplysia limacina
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-12-13 Released: 2000-06-21 
• Deposition Author(s): Federici, L., Savino, C., Musto, R., Travaglini-Allocatelli, C., Cutruzzola, F., Brunori, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.216 (Depositor) 
• R-Value Work: 
  0.189 (Depositor) 

Literature

Engineering His(E7) affects the control of heme reactivity in Aplysia limacina myoglobin.

Federici, L., Savino, C., Musto, R., Travaglini-Allocatelli, C., Cutruzzola, F., Brunori, M.

(2000) Biochem Biophys Res Commun 269: 58-63

• PubMed: 10694477 
• DOI: https://doi.org/10.1006/bbrc.2000.2259
• Primary Citation Related Structures: 
  1DM1


• PubMed Abstract: 
  

  Aplysia limacina myoglobin lacks the distal histidine (His (E7)) and displays a ligand stabilization mechanism based on Arg(E10). The double mutant Val(E7)His-Arg(E10)Thr has been prepared to engineer the role of His(E7), typical of mammalian myoglobins, in a different globin framework. The 2.0 A crystal structure of Val(E7)His-Arg(E10)Thr met-Mb mutant reveals that the His(E7) side chain points out of the distal pocket, providing an explanation for the observed failure to stabilize the Fe(II) bound oxygen in the ferrous myoglobin. Moreover, spectroscopic analysis together with kinetic data on azide binding to met-myoglobin are reported and discussed in terms of the presence of a water molecule at coordination distance from the heme iron.

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Organizational Affiliation: 
• Department of Biochemical Sciences "A. Rossi Fanelli" and C.N.R. Center for Molecular Biology, University of Rome "La Sapienza", Piazzale Aldo Moro 5, Rome, 00185, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.94 kDa 
• Atom Count: 1,199 
• Modeled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOGLOBIN	A	146	Aplysia limacina	Mutation(s): 2
UniProt
Find proteins for P02210 (Aplysia limacina) Explore P02210  Go to UniProtKB:  P02210

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.216 (Depositor) 
• R-Value Work:  0.189 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.73	α = 90
b = 89.73	β = 90
c = 92.08	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-06-21 
Deposition Author(s): Federici, L., Savino, C., Musto, R., Travaglini-Allocatelli, C., Cutruzzola, F., Brunori, M.

Revision History  

• Version 1.0: 2000-06-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection