[English] 日本語
![](img/lk-miru.gif)
- PDB-8e6h: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8e6h | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter A47W mutant in an occluded, manganese-bound state | ||||||
![]() | Divalent metal cation transporter MntH | ||||||
![]() | METAL TRANSPORT / Membrane protein / divalent transition metal importer / LeuT fold / NRAMP family | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ray, S. / Gaudet, R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 177.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 139.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8e5sSC ![]() 8e5vC ![]() 8e60C ![]() 8e6iC ![]() 8e6lC ![]() 8e6mC ![]() 8e6nC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48038.520 Da / Num. of mol.: 1 / Mutation: A47W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: mntH, DR_1709 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 105 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-OLC / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 42.55 % / Description: 20 micron in size |
---|---|
Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 7.2 Details: 20% PEG550 MME, 0.1 M HEPES, pH 7.2, 0.25 M sodium chloride, 10 mM manganese chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 13, 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: 2.39→45.35 Å / Num. obs: 16773 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.33 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.097 / Rrim(I) all: 0.191 / Net I/σ(I): 7.1 / Num. measured all: 60857 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 8E5S Resolution: 2.39→45.35 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.09 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.04 Å2 / Biso mean: 50.379 Å2 / Biso min: 22.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→45.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|