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- PDB-7b1s: Crystal structure of the ethyl-coenzyme M reductase from Candidat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b1s | |||||||||
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Title | Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum at 0.994-A resolution | |||||||||
![]() | (Ethyl-Coenzyme M reductase ...) x 3 | |||||||||
![]() | TRANSFERASE / Ethyl-CoM reductase / Methyl-CoM reductase / ethane-oxidizers / F430-cofactor / post-translational modification / gas channel / coenzyme M / coenzyme B / true atomic resolution / thermophile / archaea. | |||||||||
Function / homology | 1-THIOETHANESULFONIC ACID / : / : / Coenzyme B / Dimethylated-F430 cofactor / Chem-UUT![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wagner, T. / Lemaire, O.N. / Engilberge, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a key enzyme for anaerobic ethane activation. Authors: Hahn, C.J. / Lemaire, O.N. / Kahnt, J. / Engilberge, S. / Wegener, G. / Wagner, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 975.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7b2cC ![]() 7b2hC ![]() 5a8wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Ethyl-Coenzyme M reductase ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 66344.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Seven post-translational modifications exist in this subunit: N1-methylhistidine291 5(S)-methylarginine305 S-methylcysteine354 3-methylisoleucine377 2(S)-methylglutamine445 Thioglycine490 N2-methylhistidine491 Source: (natural) ![]() Cell line: / / Organ: / / Plasmid details: Enrichment culture / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase #2: Protein | Mass: 49874.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Cell line: / / Organ: / / Plasmid details: Enrichment culture / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase #3: Protein | Mass: 30578.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Cell line: / / Organ: / / Plasmid details: Enrichment culture / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase |
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-Non-polymers , 10 types, 3111 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/USN.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/UUT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/USN.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/UUT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-MN / | #7: Chemical | ChemComp-K / #8: Chemical | ChemComp-CL / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % / Description: Yellow brick of 250 um long. |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystals were obtained by initial screening at 20 degree celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization ...Details: Crystals were obtained by initial screening at 20 degree celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor, crystallization drop contained a mixture of 0.6 ul protein at 16.22 mg.ml-1 and 0.6 ul precipitant. The crystal was obtained by initial screening using the JBScreen Pentaerythritol screen from Jena Bioscience in a Coy tent under an N2/H2 atmosphere (95:5 %). The crystallization reservoir contained 45 % (w/v) Pentaerythritol Propoxylate (5/4 PO/OH), 100 mM Tris pH 8.5 and 400 mM potassium chloride. PH range: 7.5 - 8.5 / Temp details: / |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 8, 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: 0.992→108.19 Å / Num. obs: 1061996 / % possible obs: 89.1 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 0.992→1.07 Å / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 53103 / CC1/2: 0.563 / Rpim(I) all: 0.476 / Rrim(I) all: 1.262 / % possible all: 58.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A8W Resolution: 0.992→39.76 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.99 / Stereochemistry target values: ML Details: Refinement was performed with hydrogens in riding positions
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.64 Å2 / Biso mean: 10.6019 Å2 / Biso min: 3.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.992→39.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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