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Yorodumi- PDB-6qek: Putative membrane tansporter, magnetosome protein MamM CTD [Desul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qek | ||||||
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Title | Putative membrane tansporter, magnetosome protein MamM CTD [Desulfamplus magnetovallimortis BW-1] | ||||||
Components | Magnetosome protein | ||||||
Keywords | TRANSPORT PROTEIN / Bacterial organelle / cation diffusion facilitators / iron transport / magnetosome biogenesis / structure-function analysis. | ||||||
Function / homology | Cation efflux protein, cytoplasmic domain / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family / monoatomic cation transmembrane transporter activity / membrane => GO:0016020 / Magnetosome protein Function and homology information | ||||||
Biological species | Desulfamplus magnetovallimortis BW-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Keren, N.K. / Zarivach, R.Z. | ||||||
Funding support | Israel, 1items
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Citation | Journal: To Be Published Title: Putative membrane tansporter, magnetosome protein MamM CTD [Desulfamplus magnetovallimortis BW-1] Authors: Keren, N.K. / Zarivach, R.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qek.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qek.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qek_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 6qek_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 6qek_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6qek_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qek ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qek | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 8922.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfamplus magnetovallimortis BW-1 (bacteria) Gene: mamM Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: G8IQT5 #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: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 25% PEG 3,350 0.1M BIS-TRIS pH 5.5 0.2M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.85→40.72 Å / Num. obs: 13784 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.4 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.95 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MamM CTD MSR-1 Resolution: 1.95→40.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.153 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.845 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→40.72 Å
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Refine LS restraints |
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