+Open data
-Basic information
Entry | Database: PDB / ID: 6g64 | |||||||||
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Title | MamM CTD H264A-E289A | |||||||||
Components | Magnetosome protein MamM | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Barber-Zucker, S. / Zarivach, R. | |||||||||
Funding support | Israel, 2items
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Citation | Journal: Febs J. / Year: 2019 Title: Metal binding to the dynamic cytoplasmic domain of the cation diffusion facilitator (CDF) protein MamM induces a 'locked-in' configuration. Authors: Barber-Zucker, S. / Hall, J. / Mangapuram, S.V. / Kass, I. / Kolusheva, S. / MacMillan, F. / Zarivach, R. / Henn, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g64.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g64.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g64_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 6g64_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 6g64_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 6g64_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/6g64 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/6g64 | HTTPS FTP |
-Related structure data
Related structure data | 6g55C 6g5eC 6g6iC 3w5xS 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: 11785.293 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 BL21(DE3) (bacteria) / Variant (production host): Rosette / 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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH=5.5, 22% PEG 3350, 12.7 uM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 7559 / % possible obs: 97.2 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.014 / Rrim(I) all: 0.042 / Χ2: 0.963 / Net I/σ(I): 16.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 1.9→47.54 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.002 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.154 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.34 Å2 / Biso mean: 26.269 Å2 / Biso min: 12.61 Å2
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Refinement step | Cycle: final / Resolution: 1.9→47.54 Å
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LS refinement shell | Resolution: 1.904→1.953 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 37.694 Å / Origin y: 14.497 Å / Origin z: -0.273 Å
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