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Yorodumi- PDB-4iys: Structural and ligand binding properties of the Bateman domain of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iys | ||||||
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Title | Structural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4 | ||||||
Components | Metal transporter CNNM2 | ||||||
Keywords | METAL TRANSPORT / CBS DOMAIN / BATEMAN domain / Magnesium transporter / Magnesium sensor / cytosol | ||||||
Function / homology | Function and homology information magnesium ion homeostasis / magnesium ion transmembrane transporter activity / basolateral plasma membrane / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Corral-Rodriguez, M.A. / Stuiver, M. / Encinar, J.A. / Spiwok, V. / Gomez-Garcia, I. / Oyenarte, I. / Ereno-Orbea, J. / Terashima, H. / Accardi, A. / Diercks, T. ...Corral-Rodriguez, M.A. / Stuiver, M. / Encinar, J.A. / Spiwok, V. / Gomez-Garcia, I. / Oyenarte, I. / Ereno-Orbea, J. / Terashima, H. / Accardi, A. / Diercks, T. / Muller, D. / Martinez-Cruz, L.A. | ||||||
Citation | Journal: To be Published Title: Structural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4 Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Encinar, J.A. / Spiwok, V. / Gomez-Garcia, I. / Oyenarte, I. / Ereno-Orbea, J. / Terashima, H. / Accardi, A. / Diercks, T. / Muller, D. / Martinez-Cruz, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iys.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iys.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 4iys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/4iys ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iys | 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: 17866.381 Da / Num. of mol.: 1 / Fragment: CBS domain, UNP residues 430-584 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM2 / Plasmid: pET101D/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H8M5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 4.6 Details: 60mM NaH2PO4, 1.34M K2HPO4, pH 4.6, VAPOR DIFFUSION, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9723 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2011 |
Radiation | Monochromator: ID23-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9723 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→54 Å / Num. all: 18265 / Num. obs: 18265 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.667 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.83 / Phase error: 28.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.214 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.37 Å2 / Biso mean: 38.1368 Å2 / Biso min: 10.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.667 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -11.5967 Å / Origin y: 0.9071 Å / Origin z: -20.2802 Å
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Refinement TLS group | Selection details: all |