[English] 日本語
![](img/lk-miru.gif)
- PDB-8a8d: ATP sulfurylase from Methanothermococcus thermolithotrophicus - m... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a8d | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | ATP sulfurylase from Methanothermococcus thermolithotrophicus - monoclinic form | |||||||||
![]() | ATP sulfurylase from Methanothermococcus thermolithotrophicus | |||||||||
![]() | TRANSFERASE / Sulfate-assimilation / methanogens / archaea / APS / thermophile / methane / ATP / activation / marine / pyrophosphate | |||||||||
Function / homology | ACETATE ION![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jespersen, M. / Wagner, T. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus. Authors: Jespersen, M. / Wagner, T. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 328.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 267.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a8gC ![]() 8a8hC ![]() 8a8kC ![]() 8a8oC ![]() 1v47S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44719.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) ![]() Strain: DSM 2095 / Tissue: / / Cell: / / Cell line: / / Gene: sat / Organ: / / Variant: / / Plasmid: pET28a(+) Details (production host): Synthetic gene was cloned in pET28a(+) by using the restriction sites NdeI and BamHI with a stop codon (TGA) incorporated before BamHI Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 373 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-EDO / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % Description: Transparent, long but thin plate-shaped crystals appeared after a few weeks |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MtATPS in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol (0.7 ul) at a concentration of 27 mg.ml-1 was mixed with 0.7 ul reservoir solution. Crystals were obtained in the following crystallization ...Details: MtATPS in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol (0.7 ul) at a concentration of 27 mg.ml-1 was mixed with 0.7 ul reservoir solution. Crystals were obtained in the following crystallization condition: 20 % w/v polyethylene glycol 8000, 100 mM MES pH 6.0 and 200 mM Calcium acetate. PH range: / / Temp details: 291 K +/- 1 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→65.94 Å / Num. obs: 41069 / % possible obs: 95.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.055 / Rrim(I) all: 0.146 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2053 / CC1/2: 0.57 / Rpim(I) all: 0.475 / Rrim(I) all: 1.246 / % possible all: 98.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1V47 Resolution: 2.1→52.28 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML Details: The final cycles of refinement were performed with hydrogens in riding position, without applying non-crystallography symmetry and with translational-liberation screw.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.56 Å2 / Biso mean: 39.0955 Å2 / Biso min: 17.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→52.28 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|