+Open data
-Basic information
Entry | Database: PDB / ID: 6h8i | |||||||||
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Title | MamM CTD H285D | |||||||||
Components | Magnetosome protein MamM, Cation efflux protein family | |||||||||
Keywords | METAL TRANSPORT / Cation diffusion facilitator / magnetotactic bacteria | |||||||||
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: 1.4 Å | |||||||||
Authors | Barber-Zucker, S. / Zarivach, R. | |||||||||
Funding support | Israel, 2items
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Citation | Journal: To Be Published Title: MamM CTD H285D Authors: Barber-Zucker, S. / Zarivach, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h8i.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h8i.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 6h8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/6h8i ftp://data.pdbj.org/pub/pdb/validation_reports/h8/6h8i | HTTPS FTP |
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-Related structure data
Related structure data | 3w5xS S: Starting model for refinement |
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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: 11887.339 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-BME / | #4: 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: 1.91 Å3/Da / Density % sol: 35.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M (NH4)2SO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976247 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→47.06 Å / Num. obs: 18410 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 858 / CC1/2: 0.639 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 1.4→47.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.373 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.97 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→47.06 Å
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Refine LS restraints |
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