+Open data
-Basic information
Entry | Database: PDB / ID: 5i4k | |||||||||
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Title | Metal ABC transporter from Listeria monocytogenes with manganese | |||||||||
Components | Manganese-binding lipoprotein MntA | |||||||||
Keywords | METAL BINDING PROTEIN / structural genomics / IDP02508 / Metal ABC transporter / manganese / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information metal ion transport / cell adhesion / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes EGD-e (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å | |||||||||
Authors | Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: to be published Title: Metal ABC transporter from Listeria monocytogenes with manganese Authors: Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i4k.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i4k.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i4k_validation.pdf.gz | 414.5 KB | Display | wwPDB validaton report |
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Full document | 5i4k_full_validation.pdf.gz | 414.5 KB | Display | |
Data in XML | 5i4k_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5i4k_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/5i4k ftp://data.pdbj.org/pub/pdb/validation_reports/i4/5i4k | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32564.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: mntA, lmo1847 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y653 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #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: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 8000, 0.2 M manganese chloride, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 5, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→32.4 Å / Num. obs: 25812 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.111 / Net I/av σ(I): 19.165 / Net I/σ(I): 9.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→32.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.973 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.11 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.36 Å2 / Biso mean: 26.583 Å2 / Biso min: 15.36 Å2
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Refinement step | Cycle: final / Resolution: 1.79→32.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.837 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 48.4838 Å / Origin y: 27.4851 Å / Origin z: 46.5028 Å
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