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- PDB-1ei3: CRYSTAL STRUCTURE OF NATIVE CHICKEN FIBRINOGEN -

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Basic information

Entry
Database: PDB / ID: 1ei3
TitleCRYSTAL STRUCTURE OF NATIVE CHICKEN FIBRINOGEN
Components(FIBRINOGEN) x 3
KeywordsBLOOD CLOTTING / coiled coils / disulfide rings / fibrin forming entities
Function / homology
Function and homology information


fibrinogen complex / blood coagulation, fibrin clot formation / protein polymerization / cell-matrix adhesion / platelet activation / platelet aggregation / protein-macromolecule adaptor activity / collagen-containing extracellular matrix / signaling receptor binding / extracellular space / metal ion binding
Similarity search - Function
Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 ...Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Fibrinogen gamma chain / Fibrinogen alpha chain / Fibrinogen beta chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 5.5 Å
AuthorsYang, Z. / Mochalkin, I. / Veerapandian, L. / Riley, M. / Doolittle, R.F.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of native chicken fibrinogen at 5.5-A resolution.
Authors: Yang, Z. / Mochalkin, I. / Veerapandian, L. / Riley, M. / Doolittle, R.F.
#1: Journal: Nature / Year: 1997
Title: Crystal Structures of Fragment D from Human Fibrinogen and its Crosslinked Countepart from Fibrin
Authors: Spraggon, G. / Everse, S.J. / Doolittle, R.F.
#2: Journal: Biochemistry / Year: 1998
Title: Crystal Structure of Fragment Double-D from Human Fibrin with Two Different Bound Ligands
Authors: Everse, S.J. / Spraggon, G. / Veerapandian, L. / Riley, M. / Doolittle, R.F.
History
DepositionFeb 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRINOGEN
B: FIBRINOGEN
C: FIBRINOGEN
D: FIBRINOGEN
E: FIBRINOGEN
F: FIBRINOGEN


Theoretical massNumber of molelcules
Total (without water)308,3256
Polymers308,3256
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.726, 101.849, 210.232
Angle α, β, γ (deg.)90.0, 106.710, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBRINOGEN / / Coordinate model: Cα atoms only


Mass: 54288.000 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue fraction: BLOOD PLASMA / References: UniProt: P14448
#2: Protein FIBRINOGEN / / Coordinate model: Cα atoms only


Mass: 52874.277 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue fraction: BLOOD PLASMA / References: UniProt: Q02020
#3: Protein FIBRINOGEN / / Coordinate model: Cα atoms only


Mass: 47000.098 Da / Num. of mol.: 2 / Fragment: GAMMA CHAIN / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue fraction: BLOOD PLASMA / References: UniProt: O93568

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: PEG 3350, imidazole, calcium chloride, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.15 M1dropNaCl
30.05 Mimidazole1drop
43-4 %(v/v)PEG33501reservoir
50.05 Mimidazole1reservoir
62 mM1reservoirCaCl2
71 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.04
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 5→50 Å / Num. all: 113182 / Num. obs: 45940 / % possible obs: 80 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5
Reflection
*PLUS
Num. obs: 16412 / Num. measured all: 45940
Reflection shell
*PLUS
Highest resolution: 5.5 Å / Lowest resolution: 5.9 Å / % possible obs: 65.4 %

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Processing

Software
NameClassification
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementHighest resolution: 5.5 Å
Refinement stepCycle: LAST / Highest resolution: 5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 0 0 1896
Refinement
*PLUS
Highest resolution: 5.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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