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Yorodumi- PDB-8e5s: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e5s | ||||||
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Title | X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an occluded state | ||||||
Components | Divalent metal cation transporter MntH | ||||||
Keywords | METAL TRANSPORT / Membrane protein / divalent transition metal importer / LeuT fold / NRAMP family | ||||||
Function / homology | Function and homology information manganese ion transport / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / symporter activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Ray, S. / Gaudet, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2023 Title: High-resolution structures with bound Mn 2+ and Cd 2+ map the metal import pathway in an Nramp transporter. Authors: Ray, S. / Berry, S.P. / Wilson, E.A. / Zhang, C.H. / Shekhar, M. / Singharoy, A. / Gaudet, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e5s.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e5s.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 8e5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/8e5s ftp://data.pdbj.org/pub/pdb/validation_reports/e5/8e5s | HTTPS FTP |
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-Related structure data
Related structure data | 8e5vC 8e60C 8e6hC 8e6iC 8e6lC 8e6mC 8e6nC 6c3iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44576.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: mntH, DR_1709 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RTP8 |
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-Non-polymers , 6 types, 78 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | ChemComp-OLC / ( #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % / Description: 30 micron in size and isomorphous |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 6.7 Details: 28% PEG400, 0.1 M MES, pH 6.7, 50 mM succinic acid, pH 6.0, 5 mM spermidine, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.984 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 1, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.38→41.06 Å / Num. obs: 15678 / % possible obs: 93.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.099 / Rrim(I) all: 0.218 / Net I/σ(I): 7.4 / Num. measured all: 71063 / Scaling rejects: 210 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4.4 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6C3I Resolution: 2.38→41.06 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.28 Å2 / Biso mean: 48.0864 Å2 / Biso min: 22.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.38→41.06 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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