+Open data
-Basic information
Entry | Database: PDB / ID: 3w62 | ||||||
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Title | MamM-CTD E289A | ||||||
Components | Magnetosome protein MamM | ||||||
Keywords | METAL TRANSPORT / cation diffusion diffusion (CDF) / divalent metal cation / METAL ION TRANSPORT | ||||||
Function / homology | Function and homology information magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Zeytuni, N. / Davidov, G. / Zarivach, R. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Cation diffusion facilitators transport initiation and regulation is mediated by cation induced conformational changes of the cytoplasmic domain Authors: Zeytuni, N. / Uebe, R. / Maes, M. / Davidov, G. / Baram, M. / Raschdorf, O. / Nadav-Tsubery, M. / Kolusheva, S. / Bitton, R. / Goobes, G. / Friedler, A. / Miller, Y. / Schuler, D. / Zarivach, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w62.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w62.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 3w62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/3w62 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w62 | HTTPS FTP |
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-Related structure data
Related structure data | 3w5xSC 3w5yC 3w5zC 3w60C 3w61C 3w63C 3w64C 3w65C 3w66C 3w8pC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11928.480 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: E289A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Strain: MSR-1 / Gene: mamM, mgI491, MGR_4095 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS | ||
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#2: Chemical | #3: 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: 1.96 Å3/Da / Density % sol: 37.26 % / Mosaicity: 0.371 ° |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: 33% PEG 4000, 0.25M AmSO4, pH 8, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→50 Å / Num. obs: 11843 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.043 / Χ2: 0.971 / Net I/σ(I): 15.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 1.64→47.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2139 / WRfactor Rwork: 0.1911 / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8614 / SU B: 3.695 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0894 / SU Rfree: 0.0872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.54 Å2 / Biso mean: 26.1651 Å2 / Biso min: 9.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→47.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.639→1.682 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.0419 Å / Origin y: 14.6151 Å / Origin z: -0.2182 Å
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