[English] 日本語
Yorodumi- PDB-7cfi: Structure of the CBS domain of the bacterial CNNM/CorC family Mg2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cfi | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the CBS domain of the bacterial CNNM/CorC family Mg2+ transporter in complex with ATP | ||||||
Components | Hemolysin | ||||||
Keywords | TRANSPORT PROTEIN / transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus parvatiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Huang, Y. / Jin, F. / Hattori, M. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Structural basis for the Mg 2+ recognition and regulation of the CorC Mg 2+ transporter. Authors: Huang, Y. / Jin, F. / Funato, Y. / Xu, Z. / Zhu, W. / Wang, J. / Sun, M. / Zhao, Y. / Yu, Y. / Miki, H. / Hattori, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7cfi.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7cfi.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/7cfi ftp://data.pdbj.org/pub/pdb/validation_reports/cf/7cfi | HTTPS FTP |
---|
-Related structure data
Related structure data | 7cffC 7cfgC 7cfhSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16404.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus parvatiensis (bacteria) / Gene: AV541_07030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A109QFA5 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 66.87 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1 M CaCl2, 0.1 M HEPES pH 7.5 and 5% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→43.65 Å / Num. obs: 10115 / % possible obs: 98.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 66.48 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.45→2.65 Å / Num. unique obs: 1293 / CC1/2: 0.515 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CFH Resolution: 2.45→43.65 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4 / 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: 2.45→43.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|