+Open data
-Basic information
Entry | Database: PDB / ID: 1rjx | ||||||
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Title | Human PLASMINOGEN CATALYTIC DOMAIN, K698M MUTANT | ||||||
Components | PlasminogenPlasmin | ||||||
Keywords | HYDROLASE / microplasminogen / plasminogen activation / streptokinase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Terzyan, S. / Wakeham, N. / Zhai, P. / Rodgers, K. / Zhang, X.C. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Characterization of Lys-698 to met substitution in human plasminogen catalytic domain Authors: Terzyan, S. / Wakeham, N. / Zhai, P. / Rodgers, K. / Zhang, X.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rjx.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rjx.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1rjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/1rjx ftp://data.pdbj.org/pub/pdb/validation_reports/rj/1rjx | HTTPS FTP |
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-Related structure data
Related structure data | 1ddjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27037.061 Da / Num. of mol.: 1 / Fragment: Serine Protease CATALYTIC DOMAIN / Mutation: K698M, R561A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: PLG / Plasmid: pet11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00747, plasmin | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: hanging drop / pH: 5.6 Details: Li2SO4, Na citrate, pH 5.6, hanging drop, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2002 / Details: Blue Osmic optics |
Radiation | Monochromator: Osmic optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.725 Å / Num. obs: 15398 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3 / Num. unique all: 1507 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.32 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS Highest resolution: 2.32 Å / % possible obs: 100 % / Num. unique obs: 1507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DDJ Resolution: 2.3→45.725 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 57.8587 Å2 / ksol: 0.373242 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.725 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.246 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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