+Open data
-Basic information
Entry | Database: PDB / ID: 1gvl | ||||||
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Title | Human prokallikrein 6 (hK6)/ prozyme/ proprotease M/ proneurosin | ||||||
Components | KALLIKREIN 6 | ||||||
Keywords | HYDROLASE / ZYMOGEN / HUMAN KALLIKREIN | ||||||
Function / homology | Function and homology information positive regulation of G protein-coupled receptor signaling pathway / tissue regeneration / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / intercellular bridge / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...positive regulation of G protein-coupled receptor signaling pathway / tissue regeneration / cornified envelope / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / intercellular bridge / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gomis-Ruth, F.X. / Bayes, A. / Sotiropoulou, G. / Pampalakis, G. / Tsetsenis, T. / Villegas, V. / Aviles, F.X. / Coll, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The Structure of Human Prokallikrein 6 Reveals a Novel Activation Mechanism for the Kallikrein Family. Authors: Gomis-Ruth, F.X. / Bayes, A. / Sotiropoulou, G. / Pampalakis, G. / Tsetsenis, T. / Villegas, V. / Aviles, F.X. / Coll, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "AB" ON SHEET RECORDS BELOW ARE ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "AB" ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS. THESE ARE REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gvl.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gvl.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 1gvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gvl_validation.pdf.gz | 366.7 KB | Display | wwPDB validaton report |
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Full document | 1gvl_full_validation.pdf.gz | 371.2 KB | Display | |
Data in XML | 1gvl_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1gvl_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvl ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvl | HTTPS FTP |
-Related structure data
Related structure data | 1npmS 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: 24517.838 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): PPIC9 / References: UniProt: Q92876 |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 |
Detector | Type: ADSC/MAR RESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→38.6 Å / Num. obs: 19445 / % possible obs: 94 % / Redundancy: 3.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7 / % possible all: 90.1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. measured all: 64722 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 90.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NPM Resolution: 1.8→33.2 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CHYMOTRYPSINOGEN A (CTGA) NUMBERING APPLIED.
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Refinement step | Cycle: LAST / Resolution: 1.8→33.2 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |