[English] 日本語
![](img/lk-miru.gif)
- PDB-8cns: The Hybrid Cluster Protein from the thermophilic methanogen Metha... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8cns | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The Hybrid Cluster Protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus in a mixed redox state after soaking with hydroxylamine, at 1.36-A resolution. | |||||||||
![]() | Hybrid cluster protein from Methanothermococcus thermolithotrophicus | |||||||||
![]() | OXIDOREDUCTASE / Hybrid cluster / prismane protein / Hybrid cluster protein / methanogenic archaea / anaerobic biochemistry / thermophile / metallocluster / Nitric oxide reductase / hydroxylamine | |||||||||
Function / homology | ACETATE ION / FORMIC ACID / HYDROXYAMINE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / hybrid cluster![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lemaire, O.N. / Wagner, T. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Authors: Lemaire, O.N. / Belhamri, M. / Wagner, T. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 263.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 44.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cnrC 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: 60367.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Compared to the automatic annotation, the sequence has a five-residue extension in its N-terminal (MRPSK). The cysteine 402 has a thiol addition in its oxidized state. Source: (natural) ![]() Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: hydroxylamine reductase |
---|
-Non-polymers , 14 types, 666 molecules ![](data/chem/img/HOA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/VQ8.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/VQ8.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HOA / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-SF4 / | #6: Chemical | ChemComp-SF3 / | #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-PG5 / | #10: Chemical | ChemComp-GOL / | #11: Chemical | ChemComp-TRS / | #12: Chemical | ChemComp-VQ8 / | #13: Chemical | ChemComp-ACT / #14: Chemical | ChemComp-MRD / ( | #15: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % Description: Brown orthorhombic rod. Appeared after few weeks. |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Crystallisation was performed anaerobically by initial screening at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a ...Details: Crystallisation was performed anaerobically by initial screening at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a N2/H2 (97:3%) atmosphere. The reservoir chamber was filled with 90 ul of crystallisation condition, and the crystallisation drop was formed by spotting 0.55 ul protein with 0.55 ul of 20% (w/v) PEG 3,350 and 200 mM Magnesium formate. The protein was crystallised at 9.9 mg/ml in 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% (v/v) glycerol. Densities in the electron density map suggest a contamination of another crystallisation condition spatially close and containing 30% (v/v) 2-Methyl-2,4-pentanediol, 20 mM Calcium chloride and 100 mM Sodium acetate, pH 4.6. The crystal was soaked for 5.7 min in a solution of 100 mM hydroxylamine/HCl in the crystallisation condition and then soaked in the crystallisation solution supplemented with 20% v/v ethylene glycol for a few seconds before freezing in liquid nitrogen. PH range: / / Temp details: / |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.356→70.645 Å / Num. obs: 89372 / % possible obs: 94.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.043 / Rrim(I) all: 0.118 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.356→1.476 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4469 / CC1/2: 0.611 / Rpim(I) all: 0.472 / Rrim(I) all: 1.165 / % possible all: 67.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: Refinement steps were performed by considering all atoms anisotropic. The model was refined with hydrogens in riding position. Hydrogens were omitted in the final deposited model.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→51.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|