1MBA

APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • Primary Citation of Related Structures:  

  • 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 mole ...

    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.


    Related Citations: 
    • 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
    • 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 --: --
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
147Aplysia limacinaMutation(s): 0 
Find proteins for P02210 (Aplysia limacina)
Go to UniProtKB:  P02210
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.980α = 90.00
b = 70.700β = 90.00
c = 32.500γ = 90.00
Software Package:
Software NamePurpose
EREFrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance