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- PDB-1jy2: Crystal Structure of the Central Region of Bovine Fibrinogen (E5 ... -

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Basic information

Entry
Database: PDB / ID: 1jy2
TitleCrystal Structure of the Central Region of Bovine Fibrinogen (E5 fragment) at 1.4 Angstroms Resolution
Components
  • FIBRINOGEN ALPHA CHAIN
  • FIBRINOGEN BETA CHAIN
  • FIBRINOGEN GAMMA-B CHAIN
KeywordsBLOOD CLOTTING / fibrinogen / fragment E / disulfide bonds / asymmetry / coiled-coil / beta-sheet
Function / homology
Function and homology information


blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / protein polymerization / fibrinolysis / cell-matrix adhesion / platelet aggregation / : / protein-macromolecule adaptor activity ...blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / protein polymerization / fibrinolysis / cell-matrix adhesion / platelet aggregation / : / protein-macromolecule adaptor activity / adaptive immune response / signaling receptor binding / innate immune response / extracellular space / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Fibrinogen alpha chain / Fibrinogen beta chain / Fibrinogen gamma-B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMadrazo, J. / Brown, J.H. / Litvinovich, S. / Dominguez, R. / Yakovlev, S. / Medved, L. / Cohen, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution.
Authors: Madrazo, J. / Brown, J.H. / Litvinovich, S. / Dominguez, R. / Yakovlev, S. / Medved, L. / Cohen, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Crystal Structure of Modified Bovine Fibrinogen
Authors: Brown, J.H. / Volkmann, N. / Jun, G. / Henschen-Edman, A.H. / Cohen, C.
History
DepositionSep 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AN APPROPRIATE DATABASE MATCH WAS NOT AVAILABLE FOR FIBRINOGEN ALPHA CHAIN AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: FIBRINOGEN ALPHA CHAIN
O: FIBRINOGEN BETA CHAIN
P: FIBRINOGEN GAMMA-B CHAIN
Q: FIBRINOGEN ALPHA CHAIN
R: FIBRINOGEN BETA CHAIN
S: FIBRINOGEN GAMMA-B CHAIN


Theoretical massNumber of molelcules
Total (without water)35,8046
Polymers35,8046
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-137 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.376, 66.222, 50.658
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBRINOGEN ALPHA CHAIN


Mass: 6172.894 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Proteolytic fragment / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02672*PLUS
#2: Protein FIBRINOGEN BETA CHAIN


Mass: 6253.134 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Proteolytic fragment / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02676
#3: Protein/peptide FIBRINOGEN GAMMA-B CHAIN


Mass: 5476.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Proteolytic fragment / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P12799
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: PEG 3350, Calcium chloride, Tris, Dioxane, Sodium azide, pH 8.0, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
215.0 %PEG33501reservoir
3150 mM1reservoirCaCl2
43.5 %dioxane1reservoir
53 mM1reservoirNaN3
620 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 61149 / Num. obs: 61149 / % possible obs: 99.2 % / Redundancy: 5.8 % / Rsym value: 0.058
Reflection shellResolution: 1.4→1.45 Å / Rsym value: 0.339 / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 359638 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.6 Angstrom resolution structure of bovine E5 in the orthorhombic space group

Resolution: 1.4→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2949 5 %RANDOM
Rwork0.216 ---
all-58431 --
obs-58431 94.9 %-
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.074 Å20 Å23.614 Å2
2---10.707 Å20 Å2
3---4.633 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 318 2514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.4-1.450.4112620.398X-RAY DIFFRACTION478978.2
2.09-2.390.4113000.398X-RAY DIFFRACTION614199.6
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.411 / Rfactor Rwork: 0.398

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