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Yorodumi- PDB-2any: Expression, Crystallization and the Three-dimensional Structure o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2any | |||||||||
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Title | Expression, Crystallization and the Three-dimensional Structure of the Catalytic Domain of Human Plasma Kallikrein: Implications for Structure-Based Design of Protease Inhibitors | |||||||||
Components | plasma kallikrein, light chain | |||||||||
Keywords | BLOOD CLOTTING / HYDROLASE / mutagenically deglycosyalted human plasma kallikrein protease domain / trypsin-like serine protease | |||||||||
Function / homology | Function and homology information plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / serine-type endopeptidase activity / 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: 1.4 Å | |||||||||
Authors | Tang, J. / Yu, C.L. / Williams, S.R. / Springman, E. / Jeffery, D. / Sprengeler, P.A. / Estevez, A. / Sampang, J. / Shrader, W. / Spencer, J.R. ...Tang, J. / Yu, C.L. / Williams, S.R. / Springman, E. / Jeffery, D. / Sprengeler, P.A. / Estevez, A. / Sampang, J. / Shrader, W. / Spencer, J.R. / Young, W.B. / McGrath, M.E. / Katz, B.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. Authors: Tang, J. / Yu, C.L. / Williams, S.R. / Springman, E. / Jeffery, D. / Sprengeler, P.A. / Estevez, A. / Sampang, J. / Shrader, W. / Spencer, J. / Young, W. / McGrath, M. / Katz, B.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2any.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2any.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 2any.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2any_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 2any_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 2any_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2any_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/2any ftp://data.pdbj.org/pub/pdb/validation_reports/an/2any | HTTPS FTP |
-Related structure data
Related structure data | 2anwSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27144.842 Da / Num. of mol.: 1 / Fragment: protease domain, enzymatically deglycosylated / Mutation: C122S, N21E, N72E, N113E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLKB1, KLK3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P03952, plasma kallikrein | ||||
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#2: Chemical | #3: Chemical | ChemComp-BEN / | #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: 2.33 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.5 microliter of the protein solution and 0.5 microliter of the reservoir solution (25% PEG 6000, 0.10 M MES pH 6.5) , VAPOR DIFFUSION, SITTING DROP, temperature 290.0K |
-Data collection
Diffraction | Mean temperature: 138 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 24, 2004 |
Radiation | Monochromator: Synchrotron ALS beamline 5.0.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 49687 / Num. obs: 49687 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.4→1.46 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Enzymatically deglycosylated plasma kallikrein protease domain, PDB ENTRY 2ANW Resolution: 1.4→7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Xplor polar atom force field
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Displacement parameters | Biso mean: 15 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→7 Å
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Refine LS restraints |
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