[English] 日本語
Yorodumi- PDB-6jg0: Crystal structure of the N-terminal domain single mutant (S92E) o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jg0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal domain single mutant (S92E) of the human mitochondrial calcium uniporter fused with T4 lysozyme | ||||||
Components | Endolysin,Calcium uniporter protein | ||||||
Keywords | TRANSPORT PROTEIN / 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: 2.5 Å | ||||||
Authors | Lee, Y. / Park, J. / Min, C.K. / Kang, J.Y. / Kim, T.G. / Yamamoto, T. / Kim, D.H. / Eom, S.H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of calcium channel domain Authors: Lee, Y. / Park, J. / Min, C.K. / Kang, J.Y. / Kim, T.G. / Yamamoto, T. / Kim, D.H. / Eom, S.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jg0.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jg0.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jg0_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jg0_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 6jg0_validation.xml.gz | 12 KB | Display | |
Data in CIF | 6jg0_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/6jg0 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/6jg0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29830.170 Da / Num. of mol.: 1 / Mutation: D20N, C54T, C97A,S92E Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF LYSOZYME (1-161), LINKER GS, CALCIUM UNIPORTER PROTEIN (75-165), AND TAGS LEHHHHHH 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 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3350, 5% 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 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: 2.5→50 Å / Num. obs: 11124 / % possible obs: 99.7 % / Redundancy: 4.8 % / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.619 / Num. unique obs: 586 / CC1/2: 0.607 / Rpim(I) all: 0.368 / Rrim(I) all: 0.727 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LZM, 4XTB Resolution: 2.5→42.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.92 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.417 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→42.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|