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Yorodumi- PDB-5z5o: Structure of Pycnonodysostosis disease related I249T mutant of hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z5o | ||||||
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Title | Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K | ||||||
Components | (Cathepsin K) x 2 | ||||||
Keywords | HYDROLASE / cathepsin k / cysteine protease / lysosomal / Bone disorder / Pycnodysostosis | ||||||
Function / homology | Function and homology information cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / Collagen degradation / mitophagy / collagen catabolic process / extracellular matrix disassembly / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / apical plasma membrane / immune response / external side of plasma membrane / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / extracellular space / extracellular region / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Biswas, S. / Roy, S. | ||||||
Funding support | India, 1items
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Citation | Journal: FEBS J. / Year: 2018 Title: Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T. Authors: Roy, S. / Das Chakraborty, S. / Biswas, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z5o.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z5o.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 5z5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z5o_validation.pdf.gz | 521.1 KB | Display | wwPDB validaton report |
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Full document | 5z5o_full_validation.pdf.gz | 527.4 KB | Display | |
Data in XML | 5z5o_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 5z5o_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z5o ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z5o | HTTPS FTP |
-Related structure data
Related structure data | 1by8S 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37786.508 Da / Num. of mol.: 1 / Mutation: C139S/I249T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K |
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#2: Protein | Mass: 11152.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K |
-Non-polymers , 8 types, 247 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-NA / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100mM Na-K Phosphate 6.2, 20 % MPD, 12mM (NH4)2SO4, 10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→82 Å / Num. obs: 40362 / % possible obs: 96 % / Redundancy: 2.8 % / CC1/2: 0.999 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.795 / CC1/2: 0.493 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BY8 Resolution: 1.92→52.218 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 286.84 Å2 / Biso mean: 57.5072 Å2 / Biso min: 20.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→52.218 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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