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Yorodumi- PDB-6dfd: Crystal structure of CNNM3 cyclic nucleotide-binding homology domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dfd | ||||||
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Title | Crystal structure of CNNM3 cyclic nucleotide-binding homology domain | ||||||
Components | Metal transporter CNNM3 | ||||||
Keywords | METAL TRANSPORT / beta-barrel fold / cyclic nucleotide-binding homology domain / magnesium transporter | ||||||
Function / homology | Function and homology information magnesium ion homeostasis / intracellular manganese ion homeostasis / transmembrane transporter activity / monoatomic ion transport / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å | ||||||
Authors | Kozlov, G. / Gehring, K. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg2+efflux activity. Authors: Chen, Y.S. / Kozlov, G. / Fakih, R. / Funato, Y. / Miki, H. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dfd.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dfd.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dfd_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 6dfd_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 6dfd_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 6dfd_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dfd ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dfd | HTTPS FTP |
-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: 29401.285 Da / Num. of mol.: 2 / Mutation: I516M, T591M, A623M, L651M, V669M, I670M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NE01 #2: Water | ChemComp-HOH / | |
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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: 1.68 Å3/Da / Density % sol: 26.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9773 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9773 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 32014 / % possible obs: 99.62 % / Redundancy: 28.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 27.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3117 / CC1/2: 0.662 / % possible all: 99.49 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.901→32.474 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→32.474 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 61.7563 Å / Origin y: 37.0256 Å / Origin z: 22.8207 Å
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Refinement TLS group | Selection details: all |