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Yorodumi- PDB-2yvz: Crystal structure of magnesium transporter MgtE cytosolic domain,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yvz | ||||||
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Title | Crystal structure of magnesium transporter MgtE cytosolic domain, Mg2+-free form | ||||||
Components | Mg2+ transporter MgtE | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein | ||||||
Function / homology | Function and homology information magnesium ion transport / magnesium ion transmembrane transporter activity / magnesium ion binding / protein homodimerization activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.9 Å | ||||||
Authors | Hattori, M. / Tanaka, Y. / Fukai, S. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Crystal structure of the MgtE Mg(2+) transporter Authors: Hattori, M. / Tanaka, Y. / Fukai, S. / Ishitani, R. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yvz.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yvz.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yvz ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yvz | HTTPS FTP |
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-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: 31833.199 Da / Num. of mol.: 2 / Fragment: cytosolic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q5SMG8 |
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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: 3.037023 Å3/Da / Density % sol: 63.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2M ammonium acetate, 0.5% n-octyl-beta-D-glucopyranoside, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97909, 0.97926, 0.96403 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2007 | ||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.9→50 Å / Num. all: 7435 / Num. obs: 7435 / Net I/σ(I): 11.6 | ||||||||||||
Reflection shell | Resolution: 3.9→3.97 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.381 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.9→44.8 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 3084808.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 117.93 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 227.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.9→44.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.9→4.14 Å / Rfactor Rfree error: 0.077 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |