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Yorodumi- PDB-1l4z: X-RAY CRYSTAL STRUCTURE OF THE COMPLEX OF MICROPLASMINOGEN WITH A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l4z | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE COMPLEX OF MICROPLASMINOGEN WITH ALPHA DOMAIN OF STREPTOKINASE IN THE PRESENCE CADMIUM IONS | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / plasminogen / streptokinase / protein complex / HYDROLASE-BLOOD CLOTTING COMPLEX | ||||||
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 / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / 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 / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / 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 / plasminogen activation / 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 / protease binding / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Streptococcus dysgalactiae subsp. equisimilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Wakeham, N. / Terzyan, S. / Zhai, P. / Loy, J.A. / Tang, J. / Zhang, X.C. | ||||||
Citation | Journal: PROTEIN ENG. / Year: 2002 Title: Effects of deletion of streptokinase residues 48-59 on plasminogen activation. Authors: Wakeham, N. / Terzyan, S. / Zhai, P. / Loy, J.A. / Tang, J. / 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 | 1l4z.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l4z.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 1l4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l4z_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 1l4z_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 1l4z_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1l4z_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/1l4z ftp://data.pdbj.org/pub/pdb/validation_reports/l4/1l4z | HTTPS FTP |
-Related structure data
Related structure data | 1l4dC 1ddjS 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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Details | One molecule of microplasminogen and one molecule of streptokinase N terminal alpha domain in assymetric unit. |
-Components
#1: Protein | Mass: 27177.248 Da / Num. of mol.: 1 / Fragment: Catalytic domain, Residues 544-791 / Mutation: S741A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL12 / References: UniProt: P00747, plasmin | ||
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#2: Protein | Mass: 14907.698 Da / Num. of mol.: 1 / Fragment: N terminal alpha domain, Residues 0-147 / Mutation: Q5E, W6A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus dysgalactiae subsp. equisimilis (bacteria) Species: Streptococcus dysgalactiae / Strain: subsp. equisimilis / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00779 | ||
#3: Chemical | ChemComp-CD / #4: 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: 3.24 Å3/Da / Density % sol: 55.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na acetate, cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 26, 2001 / Details: Osmic confocal mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→24.72 Å / Num. all: 17131 / Num. obs: 17131 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 20 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 43 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 20 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1390 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Num. obs: 14317 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 100 % / Num. unique obs: 1390 / Rmerge(I) obs: 0.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DDJ Resolution: 2.8→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 41.18 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.22 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.6 |