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Yorodumi- PDB-2i9a: Crystal structure of the free aminoterminal fragment of urokinase... -
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-Basic information
Entry | Database: PDB / ID: 2i9a | ||||||
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Title | Crystal structure of the free aminoterminal fragment of urokinase type plasminogen activator (ATF) | ||||||
Components | Urokinase-type plasminogen activator | ||||||
Keywords | HYDROLASE / growth factor-like domain / kringle domain | ||||||
Function / homology | Function and homology information u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / 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: 1.9 Å | ||||||
Authors | Lubkowski, J. / Barinka, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural basis of interaction between urokinase-type plasminogen activator and its receptor. Authors: Barinka, C. / Parry, G. / Callahan, J. / Shaw, D.E. / Kuo, A. / Bdeir, K. / Cines, D.B. / Mazar, A. / Lubkowski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i9a.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i9a.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 2i9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i9a_validation.pdf.gz | 461.7 KB | Display | wwPDB validaton report |
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Full document | 2i9a_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 2i9a_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 2i9a_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/2i9a ftp://data.pdbj.org/pub/pdb/validation_reports/i9/2i9a | HTTPS FTP |
-Related structure data
Related structure data | 2i9bC 1urkS 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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Unit cell |
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Details | The biological unit is a monomer. There are 4 biological units in the asymmetric unit. |
-Components
#1: Protein | Mass: 16398.461 Da / Num. of mol.: 4 / Fragment: N-terminal fragment of urokinase, residues 21-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: P00749, u-plasminogen activator #2: Chemical | ChemComp-PO4 / #3: 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: 2.85 Å3/Da / Density % sol: 56.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 1.2 M sodium dihydrogen phosphate, 0.8 M potassium hydrogen phosphate, 200 mM lithium sulfate, 100 mM CHES, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.13539 Å |
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Jun 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.13539 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 54650 / Num. obs: 54650 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.045 / Net I/σ(I): 19.63 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 4899 / Rsym value: 0.221 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1URK Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.559 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.676 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.903→1.952 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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