+Open data
-Basic information
Entry | Database: PDB / ID: 6h84 | |||||||||
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Title | MamM CTD D249H - Cadmium form | |||||||||
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: 2.04 Å | |||||||||
Authors | Barber-Zucker, S. / Zarivach, R. | |||||||||
Funding support | Israel, 2items
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Citation | Journal: To Be Published Title: MamM CTD D249H - Cadmium form 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 | 6h84.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h84.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 6h84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h84_validation.pdf.gz | 796.6 KB | Display | wwPDB validaton report |
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Full document | 6h84_full_validation.pdf.gz | 796.5 KB | Display | |
Data in XML | 6h84_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 6h84_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/6h84 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/6h84 | HTTPS FTP |
-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: 11933.457 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 | ChemComp-BME / | ||||
#3: Chemical | #4: Chemical | ChemComp-CD / | #5: 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: 1.93 Å3/Da / Density % sol: 36.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M AmSu, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7mM CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977999 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→47.26 Å / Num. obs: 6119 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.04→2.1 Å / CC1/2: 0.603 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 2.04→47.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.081 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.164 / 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: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.017 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→47.26 Å
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Refine LS restraints |
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