+Open data
-Basic information
Entry | Database: PDB / ID: 1yc0 | ||||||
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Title | short form HGFA with first Kunitz domain from HAI-1 | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / epidermis development / rough endoplasmic reticulum / serine-type peptidase activity / extracellular matrix organization / neural tube closure / serine-type endopeptidase inhibitor activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Shia, S. / Stamos, J. / Kirchhofer, D. / Fan, B. / Wu, J. / Corpuz, R.T. / Santell, L. / Lazarus, R.A. / Eigenbrot, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Conformational lability in serine protease active sites: structures of hepatocyte growth factor activator (HGFA) alone and with the inhibitory domain from HGFA inhibitor-1B. Authors: Shia, S. / Stamos, J. / Kirchhofer, D. / Fan, B. / Wu, J. / Corpuz, R.T. / Santell, L. / Lazarus, R.A. / Eigenbrot, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yc0.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yc0.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1yc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yc0_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 1yc0_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 1yc0_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1yc0_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1yc0 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1yc0 | HTTPS FTP |
-Related structure data
Related structure data | 1ybwC 1fakS 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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-Components
#1: Protein | Mass: 30885.154 Da / Num. of mol.: 1 / Fragment: sequence database residues 373-655 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 8941.067 Da / Num. of mol.: 1 / Fragment: sequence database residues 245-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPINT1, HAI1 / Plasmid: pKD1 / Production host: Escherichia coli (E. coli) / Strain (production host): 58F3 / References: UniProt: O43278 |
#3: Chemical | ChemComp-PO4 / |
#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: 3.71 Å3/Da / Density % sol: 66.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 17975 / Num. obs: 17975 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.3 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1857 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FAK Resolution: 2.6→43.85 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.764 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: restrained atomic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 28.519 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→43.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.74 Å / Total num. of bins used: 10 /
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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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