Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15984.92 
• Atom Count: 1130 
• Residue Count: 147 
• Unique protein chains: 1

3MBA

APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION

• DOI: 10.2210/pdb3MBA/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Aplysia limacina


• Deposited: 1989-02-22 Released: 1990-01-15 
• Deposition Author(s): Bolognesi, M., Onesti, S., Gatti, G., Coda, A., Ascenzi, P., Brunori, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å

Literature

Aplysia limacina myoglobin. Crystallographic analysis at 1.6 A resolution.

Bolognesi, M., Onesti, S., Gatti, G., Coda, A., Ascenzi, P., Brunori, M.

(1989) J.Mol.Biol. 205: 529-544

• PubMed: 2926816 
• Primary Citation of Related Structures:  
  4MBA, 1MBA


• PubMed Abstract: 
  

The crystal structure of the ferric form of myoglobin from the mollusc Aplysia limacina has been refined at 1.6 A resolution, by restrained crystallographic refinement methods. The crystallographic R-factor is 0.19. The tertiary structure of the molecule conforms to the common globin fold, consisting of eight alpha-helices. The N-terminal helix A and helix G deviate significantly from linearity. The distal residue is recognized as Val63 (E7), which, however, does not contact the heme directly. Moreover the sixth (distal) co-ordination position of heme iron is not occupied by a water molecule at neutrality, i.e. below the acid-alkaline transition point of A. limacina myoglobin. The heme group sits in its crevice in the conventional orientation and no signs of heme isomerism are evident. The iron atom is 0.26 A out of the porphyrin plane, with a mean Fe-N (porphyrin) distance of 2.01 A. The co-ordination bond to the proximal histidine has a length of 2.05 A, and forms an angle of 4 degrees with the heme normal. A plane containing the imidazole ring of the proximal His intersects the heme at an angle of 29 degrees with the (porphyrin) 4N-2N direction. Inspection of the structure of pH 9.0 indicates that a hydroxyl ion is bound to the Fe sixth co-ordination position.

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Related Citations: 

• Aplysia Limacina Myoglobin. Molecular Bases for Ligand Binding and Reversible Unfolding
  Bolognesi, M.,Gatti, G.,Guanziroli, M.G.,Mattevi, A.,Onesti, S.,Coda, A.,Ascenzi, P.,Brunori, M.
  () TO BE PUBLISHED --: --
• Crystal Structure of Ferric Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution
  Bolognesi, M.,Coda, A.,Gatti, G.,Ascenzi, P.,Brunori, M.
  (1985) J.Mol.Biol. 183: 113
• Crystallization and Preliminary X-Ray Diffraction Studies on met-Myoglobin from Aplysia Limacina
  Blundell, T.L.,Brunori, M.,Curti, B.,Bolognesi, M.,Coda, A.,Fumagalli, M.,Ungaretti, L.
  (1975) J.Mol.Biol. 97: 665
• The Structure of Aplysia Limacina Myoglobin at 3.6 Angstroms Resolution
  Bolognesi, M.,Cannillo, E.,Oberti, R.,Rossi, G.,Ungaretti, L.
  (1978) Acta Crystallogr.,Sect.A (Supplement) 34: 62
• The Amino Acid Sequence of Myoglobin from the Mollusc Aplysia Limacina
  Tentori, L.,Vivaldi, G.,Carta, S.,Marinucci, M.,Massa, A.,Antonini, E.,Brunori, M.
  (1973) Int.J.Pept.Protein Res. 5: 187
• The Crystal Structure of met-Myoglobin from Aplysia Limacina at 5 Angstroms Resolution
  Ungaretti, L.,Bolognesi, M.,Cannillo, E.,Oberti, R.,Rossi, G.
  (1978) Acta Crystallogr.,Sect.B 34: 3658
• Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study
  Bolognesi, M.,Cannillo, E.,Ascenzi, P.,Giacometti, G.M.,Merli, A.,Brunori, M.
  (1982) J.Mol.Biol. 158: 305




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Organizational Affiliation: 

Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MYOGLOBIN	A	147	Aplysia limacina	Mutation(s): 0
Find proteins for P02210 (Aplysia limacina) Go to UniProtKB:  P02210

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
F	A	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 52.980	α = 90.00
b = 70.700	β = 90.00
c = 32.500	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1989-02-22 
• Released Date: 1990-01-15 
• Deposition Author(s): Bolognesi, M., Onesti, S., Gatti, G., Coda, A., Ascenzi, P., Brunori, M.

Revision History 

• Version 1.0: 1990-01-15
  Type: Initial release
• Version 1.1: 2008-03-25
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance