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Yorodumi- PDB-1m1j: Crystal structure of native chicken fibrinogen with two different... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m1j | ||||||||||||
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Title | Crystal structure of native chicken fibrinogen with two different bound ligands | ||||||||||||
Components |
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Keywords | BLOOD CLOTTING / COILED COILS / DISULFIDE RINGS / FIBRINOGEN | ||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Yang, Z. / Kollman, J.M. / Pandi, L. / Doolittle, R.F. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal Structure of Native Chicken Fibrinogen at 2.7 A Resolution Authors: Yang, Z. / Kollman, J.M. / Pandi, L. / Doolittle, R.F. #1: 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. #2: Journal: Nature / Year: 1997 Title: Crystal Sturctures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin Authors: Spraggon, G. / Everse, S.J. / Doolittle, R.F. #3: 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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Remark 999 | SEQUENCE According to the authors, the published sequence of chicken fibrinogen is incorrect. In ...SEQUENCE According to the authors, the published sequence of chicken fibrinogen is incorrect. In the alpha chain, residue 49 is GLY, not CYS. In the beta chain, residue 1 genetically must be a GLN. In the gamma chain, residue 286 is ALA, not ARG. Chains G and H mimic A16-A19 of the fibrin sequence with PRO replacing ILE A19 of the fibrin sequence. Chains I and J mimic B19-B22 of the fibrin sequence, with GLY replacing ALA B19 of the fibrin sequence. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m1j.cif.gz | 415.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m1j.ent.gz | 332.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m1j_validation.pdf.gz | 483 KB | Display | wwPDB validaton report |
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Full document | 1m1j_full_validation.pdf.gz | 571.9 KB | Display | |
Data in XML | 1m1j_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 1m1j_validation.cif.gz | 73.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1j ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1j | HTTPS FTP |
-Related structure data
Related structure data | 1fzcS S: Starting model for refinement |
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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
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 54241.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: blood / References: UniProt: P14448 #2: Protein | Mass: 52874.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: blood / References: UniProt: Q02020 #3: Protein | Mass: 46913.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: blood / References: UniProt: O93568 |
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-Protein/peptide , 2 types, 4 molecules GHIJ
#4: Protein/peptide | Mass: 426.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide is chemically synthesized. #5: Protein/peptide | Mass: 467.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide is chemically synthesized. |
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-Sugars , 2 types, 8 molecules
#6: Sugar | ChemComp-NDG / #8: Sugar | |
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-Non-polymers , 1 types, 4 molecules
#7: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2000 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. obs: 121776 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.311 / % possible all: 67.8 |
Reflection | *PLUS Highest resolution: 2.65 Å / Lowest resolution: 20 Å / Num. measured all: 1506048 |
Reflection shell | *PLUS % possible obs: 67.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FRAGMENT D FROM STRUCTURE 1FZC Resolution: 2.7→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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