+Open data
-Basic information
Entry | Database: PDB / ID: 6g5e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MamM CTD H264A-E289A-C267S | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Barber-Zucker, S. / Zarivach, R. | |||||||||
Funding support | Israel, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g5e.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g5e.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 6g5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g5e_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6g5e_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 6g5e_validation.xml.gz | 6 KB | Display | |
Data in CIF | 6g5e_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5e ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5e | HTTPS FTP |
-Related structure data
Related structure data | 6g55C 6g64C 6g6iC 3w5xS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11769.228 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): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.4 Å / Num. obs: 12814 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.013 / Rrim(I) all: 0.032 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.6→1.62 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 553 / CC1/2: 0.931 / % possible all: 86.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 1.6→35.48 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.9
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→35.48 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 37.5704 Å / Origin y: 14.614 Å / Origin z: -0.419 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: (chain A and resseq 211:292) |