+Open data
-Basic information
Entry | Database: PDB / ID: 6h9p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MamM CTD E289D - Manganese 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 MSR-1 (magnetotactic) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Barber-Zucker, S. / Zarivach, R. | |||||||||
Funding support | Israel, 2items
| |||||||||
Citation | Journal: To Be Published Title: MamM CTD E289D - Manganese form Authors: Barber-Zucker, S. / Zarivach, R. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6h9p.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6h9p.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 6h9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h9p_validation.pdf.gz | 799.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6h9p_full_validation.pdf.gz | 801.6 KB | Display | |
Data in XML | 6h9p_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 6h9p_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9p ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9p | HTTPS FTP |
-Related structure data
Related structure data | 3w5xS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _
NCS ensembles :
|
-Components
#1: Protein | Mass: 11896.372 Da / Num. of mol.: 3 / Mutation: E289D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic) Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS #2: Chemical | #3: Chemical | ChemComp-MN / | #4: Chemical | ChemComp-BME / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M LiSO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7 mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.09→44.28 Å / Num. obs: 19491 / % possible obs: 99 % / Redundancy: 17.6 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.09→2.15 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 442 / CC1/2: 0.837 / % possible all: 87.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5X Resolution: 2.1→44.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.86 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.197 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.488 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→44.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|