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Yorodumi- PDB-6tl2: Crystal structure of Eremococcus coleocola manganese transporter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tl2 | ||||||
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Title | Crystal structure of Eremococcus coleocola manganese transporter in complex with an aromatic bis-isothiourea substituted compound | ||||||
Components | Divalent metal cation transporter MntH | ||||||
Keywords | TRANSPORT PROTEIN / inhibitor complex | ||||||
Function / homology | Function and homology information cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / intracellular manganese ion homeostasis / symporter activity / cellular response to iron ion / iron ion transport / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Eremococcus coleocola ACS-139-V-Col8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Manatschal, C. / Dutzler, R. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Elife / Year: 2019 Title: Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds. Authors: Manatschal, C. / Pujol-Gimenez, J. / Poirier, M. / Reymond, J.L. / Hediger, M.A. / Dutzler, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tl2.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tl2.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 6tl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tl2_validation.pdf.gz | 572.8 KB | Display | wwPDB validaton report |
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Full document | 6tl2_full_validation.pdf.gz | 589.8 KB | Display | |
Data in XML | 6tl2_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 6tl2_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/6tl2 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/6tl2 | HTTPS FTP |
-Related structure data
Related structure data | 5m87S 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
#1: Protein | Mass: 53698.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eremococcus coleocola ACS-139-V-Col8 (bacteria) Gene: mntH, HMPREF9257_1603 / Production host: Escherichia coli (E. coli) / References: UniProt: E4KPW4 |
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#2: Chemical | ChemComp-NJZ / [ |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.17 Å3/Da / Density % sol: 76.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 50mM Tris-HCl pH 8.5 24% PEG 400 (v/v) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 21203 / % possible obs: 99.3 % / Redundancy: 14.3 % / Biso Wilson estimate: 160.35 Å2 / CC1/2: 1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.8→3.9 Å / Num. unique obs: 1606 / CC1/2: 0.817 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M87 Resolution: 3.8→12 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 171.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→12 Å
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Refine LS restraints |
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