[English] 日本語
![](img/lk-miru.gif)
- PDB-8qpm: Structure of methylene-tetrahydromethanopterin reductase from Met... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8qpm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of methylene-tetrahydromethanopterin reductase from Methanocaldococcus jannaschii | ||||||
![]() | 5,10-methylenetetrahydromethanopterin reductase | ||||||
![]() | OXIDOREDUCTASE / methylene-tetrahydropterin reductase | ||||||
Function / homology | ![]() 5,10-methylenetetrahydromethanopterin reductase / coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity / methanogenesis, from carbon dioxide / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gehl, M. / Demmer, U. / Ermler, U. / Shima, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Mutational and structural studies of ( beta alpha ) 8 -barrel fold methylene-tetrahydropterin reductases utilizing a common catalytic mechanism. Authors: Gehl, M. / Demmer, U. / Ermler, U. / Shima, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 723.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 616.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8qpjC ![]() 8qplC ![]() 8qq8C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 35836.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mer, HA335_01095 / Production host: ![]() ![]() References: UniProt: A0A832SYB5, 5,10-methylenetetrahydromethanopterin reductase #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.12 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 35% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.33 Å / Num. obs: 144127 / % possible obs: 99.84 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.822 / Num. unique obs: 14203 / CC1/2: 0.503 |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.33 Å
|