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Yorodumi- PDB-6kvx: Crystal structure of the N-terminal domain single mutant (D119A) ... -
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-Basic information
Entry | Database: PDB / ID: 6kvx | ||||||
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Title | Crystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme | ||||||
Components | Endolysin,Calcium uniporter protein, mitochondrial | ||||||
Keywords | TRANSPORT PROTEIN / MCU / mitochondrial calcium uniporter / Calcium channel | ||||||
Function / homology | Function and homology information uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission ...uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / viral release from host cell by cytolysis / calcium channel complex / peptidoglycan catabolic process / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / cell wall macromolecule catabolic process / lysozyme / protein complex oligomerization / glucose homeostasis / lysozyme activity / host cell cytoplasm / mitochondrial inner membrane / defense response to bacterium / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Lee, Y. / Park, J. / Lee, G. / Yoon, S. / Min, C.K. / Kim, T.G. / Yamamoto, T. / Kim, D.H. / Lee, K.W. / Eom, S.H. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Crystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme Authors: Lee, Y. / Park, J.S. / Kang, J.Y. / Eom, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kvx.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kvx.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kvx_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 6kvx_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 6kvx_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 6kvx_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/6kvx ftp://data.pdbj.org/pub/pdb/validation_reports/kv/6kvx | HTTPS FTP |
-Related 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: 29586.928 Da / Num. of mol.: 1 / Mutation: D20N, C54T, C97A,D119A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126, MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q8NE86, lysozyme | ||
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#2: Chemical | ChemComp-SO4 / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) polyethylene glycol (PEG) 3350, 5% (v/v) glycerol, 0.3 M (NH4)2SO4, and 0.1 M Bis-Tris-HCl (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 7820 / % possible obs: 98.7 % / Redundancy: 4.2 % / CC1/2: 0.943 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.85→2.9 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 413 / CC1/2: 0.708 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LZM, 4XTB Resolution: 2.85→28.96 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.85→28.96 Å
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LS refinement shell | Resolution: 2.85→2.923 Å / Total num. of bins used: 20
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