+Open data
-Basic information
Entry | Database: PDB / ID: 4n6l | ||||||
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Title | Crystal structure of human cystatin E/M | ||||||
Components | Cystatin-M | ||||||
Keywords | HYDROLASE INHIBITOR / cysteine protease inhibitor / legumain / asparaginyl endopeptidase / reactive center loop / papain / cathepsin / cancer / cystatin fold / protease inhibitor | ||||||
Function / homology | Function and homology information cornified envelope / cysteine-type endopeptidase inhibitor activity / anatomical structure morphogenesis / epidermis development / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å | ||||||
Authors | Dall, E. / Brandstetter, H. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Structure and mechanism of an aspartimide-dependent Peptide ligase in human legumain. Authors: Dall, E. / Fegg, J.C. / Briza, P. / Brandstetter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n6l.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n6l.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/4n6l ftp://data.pdbj.org/pub/pdb/validation_reports/n6/4n6l | HTTPS FTP |
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-Related structure data
Related structure data | 4n6mC 4n6nC 4n6oC 3gaxS 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: 14924.931 Da / Num. of mol.: 1 / Fragment: UNP residues 29-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CST6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15828 |
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#2: 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: 1.98 Å3/Da / Density % sol: 37.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30 % PEG 4000, 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→68.6 Å / Num. obs: 8955 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.95→2.06 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GAX Resolution: 1.952→36.269 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 27.59 / 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 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.952→36.269 Å
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Refine LS restraints |
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LS refinement shell |
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