+Open data
-Basic information
Entry | Database: PDB / ID: 4is5 | ||||||
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Title | Crystal Structure of the ligand-free inactive Matriptase | ||||||
Components | Suppressor of tumorigenicity 14 protein | ||||||
Keywords | HYDROLASE / Beta barrel / Serine protease / epithelium | ||||||
Function / homology | Function and homology information matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity ...matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Huang, M.D. / Zhao, B.Y. / Yuan, C. / Li, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal structures of matriptase in complex with its inhibitor hepatocyte growth factor activator inhibitor-1. Authors: Zhao, B. / Yuan, C. / Li, R. / Qu, D. / Huang, M. / Ngo, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4is5.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4is5.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 4is5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/4is5 ftp://data.pdbj.org/pub/pdb/validation_reports/is/4is5 | HTTPS FTP |
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-Related structure data
Related structure data | 4islC 4isnC 4isoC 3p8gS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26461.783 Da / Num. of mol.: 1 / Fragment: serine protease domain (unp resisdues 615-855) / Mutation: N164Q, S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS14, SNC19, ST14, TADG15 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q9Y5Y6, matriptase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GSH / | #5: 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: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCL , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→70.48 Å / Num. obs: 40678 / % possible obs: 99.44 % / Redundancy: 5.8 % |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 5.3 % / Num. unique all: 2027 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P8G Resolution: 1.48→70.48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.871 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.96 Å2 / Biso mean: 11.7613 Å2 / Biso min: 2.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→70.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Total num. of bins used: 20
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