[English] 日本語
Yorodumi- PDB-5z2i: Structure of Dictyostelium discoideum mitochondrial calcium unipo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z2i | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Dictyostelium discoideum mitochondrial calcium uniporter N-ternimal domain (Se-DdMCU-NTD) | ||||||||||||
Components | Dictyostelium discoideum mitochondrial calcium uniporter | ||||||||||||
Keywords | METAL TRANSPORT | ||||||||||||
Function / homology | Function and homology information Mitochondrial calcium ion transport / uniporter activity / uniplex complex / : / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium channel activity / mitochondrial inner membrane / calcium ion binding / mitochondrion Similarity search - Function | ||||||||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.141 Å | ||||||||||||
Authors | Yuan, Y. / Wen, M. / Chou, J. / Li, D. / Bo, O. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Acs Omega / Year: 2020 Title: Structural Characterization of the N-Terminal Domain of theDictyostelium discoideumMitochondrial Calcium Uniporter. Authors: Yuan, Y. / Cao, C. / Wen, M. / Li, M. / Dong, Y. / Wu, L. / Wu, J. / Cui, T. / Li, D. / Chou, J.J. / OuYang, B. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5z2i.cif.gz | 83 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5z2i.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 5z2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/5z2i ftp://data.pdbj.org/pub/pdb/validation_reports/z2/5z2i | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11960.181 Da / Num. of mol.: 4 / Mutation: L36M, L48M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB0186972 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q54LT0 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.73 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20%(v/v) PEG4000, 10%(v/v) 2-propanol, 0.01M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→45.77 Å / Num. obs: 19374 / % possible obs: 98.7 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.034 / Rrim(I) all: 0.105 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1416 / CC1/2: 0.723 / Rpim(I) all: 0.305 / Rrim(I) all: 0.881 / % possible all: 88.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.141→42.425 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.21 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.141→42.425 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|