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Yorodumi- PDB-1deq: THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTR... -
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-Basic information
Entry | Database: PDB / ID: 1deq | ||||||
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Title | THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION) | ||||||
Components |
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Keywords | BLOOD CLOTTING / COILED-COIL | ||||||
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 aggregation / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / innate immune response / signaling receptor binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement (using human fragment d coordinates) / Resolution: 3.5 Å | ||||||
Authors | Brown, J.H. / Volkmann, N. / Jun, G. / Henschen-Edman, A.H. / Cohen, C. | ||||||
Citation | 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. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Fibrinogen Structure in Projection at 18 Angstroms Resolution Authors: Rao, S.P.S. / Poojary, M.D. / Elliott Jr., B.W. / Melanson, L.A. / Oriel, B. / Cohen, C. #2: Journal: J.Mol.Biol. / Year: 1978 Title: Crystals of Modified Fibrinogen: Size, Shape and Packing of Molecules Authors: Weisel, J.W. / Warren, S.G. / Cohen, C. #3: Journal: J.Mol.Biol. / Year: 1977 Title: Crystalline States of a Modified Fibrinogen Authors: Tooney, N.M. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1deq.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1deq.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 1deq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1deq_validation.pdf.gz | 406.6 KB | Display | wwPDB validaton report |
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Full document | 1deq_full_validation.pdf.gz | 408.3 KB | Display | |
Data in XML | 1deq_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 1deq_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1deq ftp://data.pdbj.org/pub/pdb/validation_reports/de/1deq | HTTPS FTP |
-Related structure data
Related structure data | 1fzaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | An ~ 4 Angstrom structure of the 285 kDa major fragment of bovine fibrinogen. The alpha-carbon coordinates for both molecules per asymmetric unit are provided. The molecule is a dimer of a heterotrimer. Coordinates with chain ids ABC:DEF and NOP:QRS are the two crystallographically independent dimers. A,D,N, and Q correspond to the A-alpha chain. B,E,O, and R correspond to the B-beta chain. C,F,P, and S correspond to the gamma chain. These alpha-carbon coordinates include the end gamma and beta domains (i.e. the C-terminal globular domains of the gamma and B-beta chains, respectively) and the coiled coils (which are made of the A-alpha, B-beta, and gamma chains.). The density corresponding to the central disulfide knot region is too irregular to be traced at this resolution, and only some coordinates for part of this domain are included where density is seen (designated M and Z for the for the two molecules per a.u.). |
-Components
#1: Protein | Mass: 42767.410 Da / Num. of mol.: 4 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02672 #2: Protein | Mass: 46901.641 Da / Num. of mol.: 4 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02676 #3: Protein | Mass: 46626.605 Da / Num. of mol.: 4 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P12799 #4: Protein | Mass: 7677.455 Da / Num. of mol.: 2 / Fragment: PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT / Source method: isolated from a natural source / Details: DISORDERED DISULFIDE KNOT REGION / Source: (natural) Bos taurus (cattle) |
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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: 3.12 Å3/Da / Density % sol: 60.53 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 6.2 Details: 10 mM MES, 5mM sodium azide, 2mM calcium chloride , pH 6.2, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.4→210 Å / Num. all: 79465 / Num. obs: 79465 / % possible obs: 78.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.42 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.05 | ||||||||||||||||||||
Reflection shell | Resolution: 3.38→3.57 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Num. unique all: 6830 / % possible all: 46.7 | ||||||||||||||||||||
Reflection | *PLUS | ||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 46.7 % |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement (using human fragment d coordinates) Starting model: human fragment d coordinates (see related entry 1fza) Resolution: 3.5→10 Å / σ(F): 0 / Stereochemistry target values: modified CHARMM in X-Plor Details: Side chains were included in refinement. At this resolution, however, the correct side chain conformations cannot be generally determined, and only alpha Carbons are deposited here. A B- ...Details: Side chains were included in refinement. At this resolution, however, the correct side chain conformations cannot be generally determined, and only alpha Carbons are deposited here. A B-factor equal to 999 identifies a residue whose density is generally relatively disordered and thus is not included in refinement (but generally positioned using information from non- crystallographically-related copies). Note that of the asymmetric unit's four half-dimers, that designated by chain ids N, O, and P has the most residues included in the refinement, and its electron density is best ordered. The central disulphide knot region could not be traced, and only some coordinates for part of this domain are included (resname=UNK, chainid M and Z for the two molecules per a.u.). Due to anisotropy in the the diffraction, the data in the highest shells (esp. 4.0-3.5) are quite incomplete, and hence the structure is judged overall to at ~4.0 angstroms resolution.
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Refinement step | Cycle: LAST / Resolution: 3.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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