2PF1 image
Deposition Date 1992-09-17
Release Date 1994-01-31
Last Version Date 2025-03-26
Entry Detail
PDB ID:
2PF1
Title:
STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 ANGSTROMS RESOLUTION
Biological Source:
Source Organism:
Bos taurus (Taxon ID: 9913)
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Observed:
0.17
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:PROTHROMBIN FRAGMENT 1
Gene (Uniprot):F2
Chain IDs:A
Chain Length:156
Number of Molecules:1
Biological Source:Bos taurus
Primary Citation
Structure of bovine prothrombin fragment 1 refined at 2.25 A resolution.
J.Mol.Biol. 220 481 494 (1991)
PMID: 1856869 DOI: 10.1016/0022-2836(91)90025-2

Abstact

The structure of bovine prothrombin fragment 1 has been refined at 2.25 A resolution using high resolution measurements made with the synchrotron beam at CHESS. The synchrotron data were collected photographically by oscillation methods (R-merge = 0.08). These were combined with lower order diffractometer data for refinement purposes. The structure was refined using restrained least-squares methods with the program PROLSQ to a crystallographic R-value of 0.175. The structure includes 105 water molecules with occupancies of greater than 0.6. The first 35 residues (Ala1-Leu35) of the N-terminal gamma-carboxy glutamic acid-domain (Ala1-Cys48) of fragment 1 are disordered as are two carbohydrate chains of Mr approximately 5000; the latter two combine to render 40% of the structure disordered. The folding of the kringle of fragment 1 is related to the close intramolecular contact between the inner loop disulfide groups. Half of the conserved sequence of the kringle forms an inner core surrounding these disulfide groups. The remainder of the sequence conservation is associated with the many turns of the main chain. The Pro95 residue of the kringle has a cis conformation and Tyr74 is ordered in fragment 1, although nuclear magnetic resonance studies indicate that the comparable residue of plasminogen kringle 4 has two positions. Surface accessibility calculations indicate that none of the disulfide groups of fragment 1 is accessible to solvent.

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