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Yorodumi- PDB-2fxr: human beta tryptase II complexed with activated ketone inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fxr | ||||||
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Title | human beta tryptase II complexed with activated ketone inhibitor CRA-29382 | ||||||
Components | Tryptase beta-2 | ||||||
Keywords | HYDROLASE / serine protease / activated ketone inhibitor / pyrrolidine / CRA-29382 | ||||||
Function / homology | Function and homology information tryptase / serine-type peptidase activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Katz, B.A. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structure-guided design of Peptide-based tryptase inhibitors. Authors: McGrath, M.E. / Sprengeler, P.A. / Hirschbein, B. / Somoza, J.R. / Lehoux, I. / Janc, J.W. / Gjerstad, E. / Graupe, M. / Estiarte, A. / Venkataramani, C. / Liu, Y. / Yee, R. / Ho, J.D. / ...Authors: McGrath, M.E. / Sprengeler, P.A. / Hirschbein, B. / Somoza, J.R. / Lehoux, I. / Janc, J.W. / Gjerstad, E. / Graupe, M. / Estiarte, A. / Venkataramani, C. / Liu, Y. / Yee, R. / Ho, J.D. / Green, M.J. / Lee, C.-S. / Liu, L. / Tai, V. / Spencer, J. / Sperandio, D. / 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 | 2fxr.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fxr.ent.gz | 163.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fxr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2fxr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2fxr_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 2fxr_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/2fxr ftp://data.pdbj.org/pub/pdb/validation_reports/fx/2fxr | HTTPS FTP |
-Related structure data
Related structure data | 2fpzC 2fs8C 2fs9C 2fwwC 2fx4C 2fx6C 1a0lS 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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Unit cell |
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Details | The biological unit is the tetramer. Each asymmetric unit contains one biologically-relevant tetramer. |
-Components
#1: Protein | Mass: 27491.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPSB2, TPS2 / Production host: Pichia pastoris (fungus) / References: UniProt: P20231, tryptase #2: Chemical | ChemComp-C3A / #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: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2mg/mL protein, 10 mM MES, pH 6.1, 2M NaCl dissolved in 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution ...Details: 2mg/mL protein, 10 mM MES, pH 6.1, 2M NaCl dissolved in 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution to crystallization solution. Crystals appropriate for diffraction studies appeared in 2-5 days at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.78 Å / Num. all: 39151 / Num. obs: 39151 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.101 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.557 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A0L Resolution: 2.5→42.78 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→42.78 Å
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Refine LS restraints |
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Xplor file |
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