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Yorodumi- PDB-3gyl: Structure of Prostasin at 1.3 Angstroms resolution in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gyl | ||||||
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Title | Structure of Prostasin at 1.3 Angstroms resolution in complex with a Calcium Ion. | ||||||
Components | Prostasin | ||||||
Keywords | HYDROLASE / PROSTASIN / ENAC / ZYMOGEN / DIVALENT CATION / CHANNEL ACTIVATING / Cell membrane / Disulfide bond / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Transmembrane | ||||||
Function / homology | Function and homology information Formation of the cornified envelope / positive regulation of sodium ion transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / 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 / FOURIER SYNTHESIS / Resolution: 1.3 Å | ||||||
Authors | Spraggon, G. / Hornsby, M. / Shipway, A. / Harris, J.L. / Lesley, S.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations. Authors: Spraggon, G. / Hornsby, M. / Shipway, A. / Tully, D.C. / Bursulaya, B. / Danahay, H. / Harris, J.L. / Lesley, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gyl.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gyl.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gyl_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 3gyl_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 3gyl_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3gyl_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/3gyl ftp://data.pdbj.org/pub/pdb/validation_reports/gy/3gyl | HTTPS FTP |
-Related structure data
Related structure data | 3e0nC 3e1xSC 3fvfC 3gymC 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: 28226.553 Da / Num. of mol.: 1 Fragment: UNP residues 45-305, Peptidase S1 Domain of Prostasin heavy chain Mutation: C122S,N127Q,C170S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hCAP1, PRSS8 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 References: UniProt: Q16651, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% Peg-3000, 0.2M Calcium Acetate buffered with 0.1M Tris at pH 7.0,, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2004 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→45 Å / Num. obs: 57859 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 6.52 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5058 / Rsym value: 0.763 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3E1X Resolution: 1.3→45 Å / SU ML: 1.04 / Isotropic thermal model: anisotropic / Cross valid method: througout / σ(F): 0.12 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.487 Å2 / ksol: 0.437 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.3→45 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.4561 Å / Origin y: -0.0525 Å / Origin z: -15.8634 Å
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Refinement TLS group | Selection details: chain B |