[English] 日本語
![](img/lk-miru.gif)
- PDB-7p4v: GlnK1 from Methanothermococcus thermolithotrophicus with dADP at ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7p4v | ||||||
---|---|---|---|---|---|---|---|
Title | GlnK1 from Methanothermococcus thermolithotrophicus with dADP at a resolution of 1.94 A | ||||||
![]() | GlnK1 from Methanothermococcus thermolithotrophicus | ||||||
![]() | SIGNALING PROTEIN / PII-family / Methanococcales / methanogenic archaea / hydrogenotrophs / protein regulation / inhibitor / T-loop / conformational change / dADP / 2-oxoglutarate / nitrogen metabolism | ||||||
Function / homology | 2'-DEOXYADENOSINE-5'-DIPHOSPHATE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mueller, M.-C. / Wagner, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales . Authors: Muller, M.C. / Wagner, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 874.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 874.1 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p4yC ![]() 7p50C ![]() 7p52C ![]() 2j9dS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 14648.796 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) ![]() Strain: DSM 2095 / Tissue: / / Cell: / / Cell line: / / Gene: glnk1 / Organ: / / Variant: / / Plasmid: pET-28a(+) / Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-DAT / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.69 % / Description: transparent hexagonal rod |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: GlnK1 crystallized at a concentration of 33 mg/ml in 25 mM TrisHCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl . Drop of 0.6 ul of protein was mixed with 0.6 ul of the ...Details: GlnK1 crystallized at a concentration of 33 mg/ml in 25 mM TrisHCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl . Drop of 0.6 ul of protein was mixed with 0.6 ul of the crystallization solution in a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The reservoir contained 90 ul of the following crystallization solution: 35 % w/v Pentaerythritol propoxylate (17/8 PO/OH), 100 mM MES pH 6.5, 200 mM Ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→75.601 Å / Num. obs: 10108 / % possible obs: 89.1 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Rrim(I) all: 0.055 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.94→2.148 Å / Redundancy: 18.6 % / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 502 / CC1/2: 0.773 / Rpim(I) all: 0.403 / Rrim(I) all: 1.759 / % possible all: 60.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2J9D Resolution: 1.94→39.3 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.79 / Stereochemistry target values: ML Details: The last refinement cycle was performed with hydrogens in riding position
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.32 Å2 / Biso mean: 62.7293 Å2 / Biso min: 32.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→39.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|