1FLP

STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata. Crystallographic analysis at 1.5 A resolution.

Rizzi, M.Wittenberg, J.B.Coda, A.Fasano, M.Ascenzi, P.Bolognesi, M.

(1994) J Mol Biol 244: 86-99

  • DOI: 10.1006/jmbi.1994.1706
  • Primary Citation of Related Structures:  
    1FLP

  • PubMed Abstract: 
  • The crystal structure of the aquo-met form of the sulfide-reactive hemoglobin (component I) from the gill of the symbiont-harboring mollusc, Lucina pectinata, has been solved and refined at 1.5 A resolution, based on synchrotron radiation X-ray diffraction data, and employing molecular replacement techniques ...

    The crystal structure of the aquo-met form of the sulfide-reactive hemoglobin (component I) from the gill of the symbiont-harboring mollusc, Lucina pectinata, has been solved and refined at 1.5 A resolution, based on synchrotron radiation X-ray diffraction data, and employing molecular replacement techniques. The crystallographic R-factor, calculated for the data in the 15.0 to 1.5 A resolution range, is 0.170, with highly regular stereochemical parameters for the protein model, and including 131 water molecules. The monomeric hemoglobin I chain consists of 142 amino acid residues, which have been partly identified on the basis of the crystallographic analysis. The molecule is characterized by an unusual distribution of aromatic residues, particularly in the region surrounding the distal site in the heme pocket. The heme distal residue is Gln(64)E7, while other notable amino acid substitutions include Trp(21)B2, Phe(29)B10, Leu(46)CD3, Phe(68)E11 and Trp(75)E18. An amino acid insertion (Ser44) is observed between sites CD1 and CD2. In the aquo-met protein, a water molecule is present at the sixth coordination position of the heme iron, and hydrogen bonded to Gln(64)E7. Simple model building shows that a dioxygen molecule, bound to ferrous protein, would contact with its free atom the ring edge of Phe(29)B10, being thus stabilized at the coordination site by an aromatic-electrostatic interaction. Similarly, the unique packing and organization of aromatic residues in the surroundings of the heme distal site is proposed as the molecular basis of the very high affinity of Lucina pectinata hemoglobin I for hydrogen sulfide, considered as one of the two physiological ligands of the protein.


    Related Citations: 
    • Crystallization and Preliminary Data for the Ferric Form of Lucina Pectinata Hemoglobin I
      Casale, E., Lionetti, C., Coda, A., Merli, A., Ascenzi, P., Wittenberg, J.B., Bolognesi, M.
      (1991) J Mol Biol 222: 447
    • Hemoglobins of the Lucina Pectinata(Slash)Bacteria Symbiosis. I. Molecular Properties, Kinetics and Equilibria of Reactions with Ligands
      Kraus, D.W., Wittenberg, J.B.
      (1990) J Biol Chem 265: 16043

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEMOGLOBIN I (AQUO MET)A142Phacoides pectinatusMutation(s): 0 
UniProt
Find proteins for P41260 (Phacoides pectinatus)
Explore P41260 
Go to UniProtKB:  P41260
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.97α = 90
b = 38.39β = 97.4
c = 42.65γ = 90
Software Package:
Software NamePurpose
ARP/wARPmodel building
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance