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- PDB-2pf1: STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 2pf1
TitleSTRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 ANGSTROMS RESOLUTION
ComponentsPROTHROMBIN FRAGMENT 1
KeywordsHYDROLASE(SERINE PROTEINASE)
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / : / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsSeshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structure of bovine prothrombin fragment 1 refined at 2.25 A resolution.
Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Prothrombin Fragment 1 Refined at 2.8 Angstroms Resolution
Authors: Tulinsky, A. / Park, C.H. / Skrzypczak-Jankun, E.
#2: Journal: Biochemistry / Year: 1986
Title: Three-Dimensional Structure of the Kringle Sequence: Structure of Prothrombin Fragment 1
Authors: Park, C.H. / Tulinsky, A.
History
DepositionSep 17, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTHROMBIN FRAGMENT 1


Theoretical massNumber of molelcules
Total (without water)18,0251
Polymers18,0251
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.620, 77.620, 85.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUE PRO 95 IS A CIS PROLINE.

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Components

#1: Protein PROTHROMBIN FRAGMENT 1


Mass: 18024.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00735
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal grow
*PLUS
pH: 6.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
132 %(w/v)PEG40011
20.1 Msodium phosphate11

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Data collection

Reflection
*PLUS
Highest resolution: 2.25 Å / Num. all: 10599 / Num. obs: 8365 / % possible obs: 76 % / Observed criterion σ(F): 3

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→5 Å / Rfactor obs: 0.175 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 164 1111
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.014
X-RAY DIFFRACTIONp_angle_d0.040.053
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.054
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it10.59
X-RAY DIFFRACTIONp_mcangle_it1.51.07
X-RAY DIFFRACTIONp_scbond_it10.79
X-RAY DIFFRACTIONp_scangle_it1.51.12
X-RAY DIFFRACTIONp_plane_restr0.020.011
X-RAY DIFFRACTIONp_chiral_restr0.150.207
X-RAY DIFFRACTIONp_singtor_nbd0.50.28
X-RAY DIFFRACTIONp_multtor_nbd0.50.38
X-RAY DIFFRACTIONp_xhyhbond_nbd0.50.32
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor31.9
X-RAY DIFFRACTIONp_staggered_tor1527.8
X-RAY DIFFRACTIONp_orthonormal_tor2027.3
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 5 Å / Num. reflection all: 6364 / σ(F): 0 / Rfactor all: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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