+Open data
-Basic information
Entry | Database: PDB / ID: 1ei3 | ||||||
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Title | CRYSTAL STRUCTURE OF NATIVE CHICKEN FIBRINOGEN | ||||||
Components | (FIBRINOGEN) x 3 | ||||||
Keywords | BLOOD CLOTTING / coiled coils / disulfide rings / fibrin forming entities | ||||||
Function / homology | Function and homology information blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis ...blood coagulation, common pathway / fibrinogen complex / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / cell-matrix adhesion / platelet activation / platelet aggregation / protein-macromolecule adaptor activity / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / signaling receptor binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 5.5 Å | ||||||
Authors | Yang, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ei3.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ei3.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ei3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ei3_validation.pdf.gz | 348.3 KB | Display | wwPDB validaton report |
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Full document | 1ei3_full_validation.pdf.gz | 348.4 KB | Display | |
Data in XML | 1ei3_validation.xml.gz | 1 KB | Display | |
Data in CIF | 1ei3_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/1ei3 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/1ei3 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.75 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.04 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 29, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 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 % |
-Processing
Software |
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Refinement | Highest resolution: 5.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5.5 Å
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Refinement | *PLUS Highest resolution: 5.5 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |