+Open data
-Basic information
Entry | Database: PDB / ID: 3w60 | ||||||
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Title | MamM-CTD H264A | ||||||
Components | Magnetosome protein MamM | ||||||
Keywords | METAL TRANSPORT / cation diffusion facilitator (CDF) / divalent cation transport / 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 / molecular replacement / Resolution: 1.82 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 | 3w60.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w60.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 3w60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w60_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 3w60_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 3w60_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 3w60_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/3w60 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w60 | HTTPS FTP |
-Related structure data
Related structure data | 3w5xSC 3w5yC 3w5zC 3w61C 3w62C 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
#1: Protein | Mass: 11919.447 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: H264A 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): Rosstea / 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: 2.01 Å3/Da / Density % sol: 38.66 % / Mosaicity: 0.882 ° |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M BIS-TRIS PH 5.5, 15% PEG 3350, 0.2M AmSO4 , VAPOR DIFFUSION, SITTING DROP, temperature 100K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.82→50 Å / Num. obs: 8874 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Χ2: 1.219 / Net I/σ(I): 13.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 1.82→47.56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.3274 / WRfactor Rwork: 0.2552 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.6639 / SU B: 11.236 / SU ML: 0.154 / SU R Cruickshank DPI: 0.1654 / SU Rfree: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.172 / 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: 72.72 Å2 / Biso mean: 33.5569 Å2 / Biso min: 9.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→47.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.815→1.862 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.4799 Å / Origin y: 14.3861 Å / Origin z: -0.2916 Å
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