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Yorodumi- PDB-8e6m: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e6m | ||||||
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Title | X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an inward-open, cadmium-bound 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: 2.48 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 | 8e6m.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e6m.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 8e6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/8e6m ftp://data.pdbj.org/pub/pdb/validation_reports/e6/8e6m | HTTPS FTP |
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-Related structure data
Related structure data | 8e5sSC 8e5vC 8e60C 8e6hC 8e6iC 8e6lC 8e6nC 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
-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 , 5 types, 79 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-OLC / ( #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-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: 2.35 Å3/Da / Density % sol: 47.59 % / Description: 35 micron in size |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 6.1 Details: 24% PEG400, 0.1 M MES, pH 6.1, 50 mM succinic acid, pH 6.0, 20 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: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 6, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.48→45.54 Å / Num. obs: 15312 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 49.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.083 / Rrim(I) all: 0.184 / Net I/σ(I): 8.1 / Num. measured all: 74940 / Scaling rejects: 47 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8E5S Resolution: 2.48→45.54 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.96 / 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: 187.83 Å2 / Biso mean: 64.8177 Å2 / Biso min: 27.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→45.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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