1KFR | pdb_00001kfr

Structural plasticity in the eight-helix fold of a trematode hemoglobin

• PDB DOI: https://doi.org/10.2210/pdb1KFR/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Paramphistomum epiclitum
• Mutation(s): No 


• Deposited: 2001-11-22 Released: 2002-04-24 
• Deposition Author(s): Milani, M., Pesce, A., Dewilde, S., Ascenzi, P., Moens, L., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.220 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.161 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Structural plasticity in the eight-helix fold of a trematode haemoglobin.

Milani, M., Pesce, A., Dewilde, S., Ascenzi, P., Moens, L., Bolognesi, M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 719-722

• PubMed: 11914507 
• DOI: https://doi.org/10.1107/s0907444902001865
• Primary Citation Related Structures: 
  1KFR


• PubMed Abstract: 
  

  The three-dimensional structure of recombinant haemoglobin from the trematode Paramphistomum epiclitum, displaying the highest oxygen affinity so far observed for (non)vertebrate haemoglobins, has previously been determined at 1.17 A resolution (orthorhombic space group P2(1)2(1)2(1)). In the present communication, the three-dimensional structure of wild-type P. epiclitum haemoglobin is reported at 1.85 A resolution in a monoclinic crystal form (R factor = 16.1%, R(free) = 22.0%). Comparison of P. epiclitum (recombinant versus wild-type ferric Hb) structures in the two crystal forms shows structural differences in the haem proximal and distal sites which have not been reported for other known haemoglobin structures previously.

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Organizational Affiliation: 
• Department of Physics-INFM, Advanced Biotechnology Centre, University of Genova, Largo Rosanna Benzi 10, I-16146 Genova, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.47 kDa 
• Atom Count: 1,404 
• Modeled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin	A	147	Paramphistomum epiclitum	Mutation(s): 0
UniProt
Find proteins for P80721 (Paramphistomum epiclitum) Explore P80721  Go to UniProtKB:  P80721

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.220 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.161 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.117	α = 90
b = 31.45	β = 95.5
c = 54.952	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-24 
Deposition Author(s): Milani, M., Pesce, A., Dewilde, S., Ascenzi, P., Moens, L., Bolognesi, M.

Revision History  

• Version 1.0: 2002-04-24
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations