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Yorodumi- PDB-4dur: The X-ray Crystal Structure of Full-Length type II Human Plasminogen -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dur | |||||||||
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Title | The X-ray Crystal Structure of Full-Length type II Human Plasminogen | |||||||||
Components | PlasminogenPlasmin | |||||||||
Keywords | HYDROLASE / serine protease / fibrinolysis | |||||||||
Function / homology | Function and homology information plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Law, R.H.P. / Caradoc-Davies, T. / Whisstock, J.C. | |||||||||
Citation | Journal: Cell Rep / Year: 2012 Title: The X-ray crystal structure of full-length human plasminogen Authors: Law, R.H.P. / Caradoc-Davies, T. / Cowieson, N. / Horvath, A.J. / Quek, A.J. / Encarnacao, J.A. / Steer, D. / Cowan, A. / Zhang, Q. / Lu, B.G.C. / Pike, R.N. / Smith, A.I. / Coughlin, P.B. / Whisstock, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dur.cif.gz | 648.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dur.ent.gz | 533.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/4dur ftp://data.pdbj.org/pub/pdb/validation_reports/du/4dur | HTTPS FTP |
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-Related structure data
Related structure data | 4duuC 1krnS 1losS 1qrzS 5hpgS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 88544.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: plasma / References: UniProt: P00747, plasmin #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 1448 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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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: 3.98 Å3/Da / Density % sol: 69.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate, 0.2M sodium acetate, polyethylene glycol 1000, polyethylene glycol 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953692 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2011 / Details: Silicon mirrors (adaptive and U-bent) |
Radiation | Monochromator: Double crystal monochromator (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953692 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→125.25 Å / Num. obs: 104073 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 43.58 Å2 / Rmerge(I) obs: 0.175 / Rsym value: 0.071 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.3 / Num. unique all: 79752 / Rsym value: 0.351 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QRZ, 1KRN, 5HPG, 1LOS Resolution: 2.45→125.25 Å / Cor.coef. Fo:Fc: 0.9197 / Cor.coef. Fo:Fc free: 0.8979 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.188 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 147.84 Å2 / Biso mean: 34.1888 Å2 / Biso min: 8.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.283 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→125.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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