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Yorodumi- PDB-6g52: CRYSTAL STRUCTURE OF THE CNMP BINDING DOMAIN OF THE MAGNESIUM TRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g52 | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF THE CNMP BINDING DOMAIN OF THE MAGNESIUM TRANSPORTER CNNM4 | ||||||||||||||||||
Components | Metal transporter CNNM4 | ||||||||||||||||||
Keywords | METAL TRANSPORT / CYCLIN M4 / ACDP4 / MAGNESIUM / TRANSPORTER / JALILI SYNDROME / MAGNESIUM ABSORPTION / MAGNESIUM HOMEOSTASIS | ||||||||||||||||||
Function / homology | Function and homology information : / sodium ion transmembrane transporter activity / magnesium ion transport / magnesium ion homeostasis / magnesium ion transmembrane transporter activity / enamel mineralization / response to stimulus / transmembrane transporter activity / visual perception / basolateral plasma membrane ...: / sodium ion transmembrane transporter activity / magnesium ion transport / magnesium ion homeostasis / magnesium ion transmembrane transporter activity / enamel mineralization / response to stimulus / transmembrane transporter activity / visual perception / basolateral plasma membrane / intracellular membrane-bounded organelle / protein-containing complex / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.691 Å | ||||||||||||||||||
Authors | Gimenez, P. / Oyenarte, I. / Hardy, S. / Zubillaga, M. / Merino, N. / Blanco, F.J. / Siliqi, D. / Tremblay, M. / Muller, D. / Martinez-Cruz, L.A. | ||||||||||||||||||
Funding support | Spain, 5items
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Citation | Journal: Int J Mol Sci / Year: 2019 Title: Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4. Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Gonzalez-Recio, I. / Fernandez-Rodriguez, C. / Corral-Rodriguez, M.A. / Campos-Zarraga, I. / Simon, J. / Kostantin, E. / Hardy, S. / Diaz Quintana, A. ...Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Gonzalez-Recio, I. / Fernandez-Rodriguez, C. / Corral-Rodriguez, M.A. / Campos-Zarraga, I. / Simon, J. / Kostantin, E. / Hardy, S. / Diaz Quintana, A. / Zubillaga Lizeaga, M. / Merino, N. / Diercks, T. / Blanco, F.J. / Diaz Moreno, I. / Martinez-Chantar, M.L. / Tremblay, M.L. / Muller, D. / Siliqi, D. / Martinez-Cruz, L.A. #1: Journal: J. Biol. Chem. / Year: 2017 Title: Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2. Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / ...Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / Claverie-Martin, F. / Muller, D. / Tremblay, M.L. / Martinez-Cruz, L.A. #2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2012 Title: Purification, crystallization and preliminary crystallographic analysis of the CBS-domain pair of cyclin M2 (CNNM2). Authors: Gomez-Garcia, I. / Stuiver, M. / Ereno, J. / Oyenarte, I. / Corral-Rodriguez, M.A. / Muller, D. / Martinez-Cruz, L.A. #3: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2011 Title: Purification, crystallization and preliminary crystallographic analysis of the CBS pair of the human metal transporter CNNM4. Authors: Gomez Garcia, I. / Oyenarte, I. / Martinez-Cruz, L.A. #4: Journal: Biochem J. / Year: 2014 Title: Nucleotide binding triggers a conformational change of the CBS module of the magnesium transporter CNNM2 from a twisted towards a flat structure. Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / de Opakua, A.I. / Blanco, F.J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / ...Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / de Opakua, A.I. / Blanco, F.J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. / 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 | 6g52.cif.gz | 248 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g52.ent.gz | 202.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g52 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g52 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 21407.645 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM4, ACDP4, KIAA1592 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6P4Q7 |
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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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.5 M Sodium Formate, 5 % PEG 3350, 0.1 M TRIS pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.69→243.96 Å / Num. obs: 21343 / % possible obs: 99.7 % / Redundancy: 19.4 % / Biso Wilson estimate: 41.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.042 / Rrim(I) all: 0.184 / Χ2: 1.464 / Net I/σ(I): 13.9 / Num. measured all: 413360 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.691→63.286 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 28.99 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 253.07 Å2 / Biso mean: 100.772 Å2 / Biso min: 39.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.691→63.286 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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