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- PDB-5n1q: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n1q | ||||||
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Title | METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS AT 1.9 A RESOLUTION | ||||||
![]() | (METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ...) x 3 | ||||||
![]() | TRANSFERASE / POST-TRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / HYDROGEN BONDING / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOCOCCALES / NICKEL / OXIDATION-REDUCTION / OXIDOREDUCTASES / PHOSPHOTHREONINE / PROTEIN CONFORMATION / PROTEIN FOLDING / PROTEIN STRUCTURE / THERMOPHILE / AUTOTROPH | ||||||
Function / homology | ![]() coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wagner, T. / Wegner, C.E. / Ermler, U. / Shima, S. | ||||||
![]() | ![]() Title: Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales. Authors: Wagner, T. / Wegner, C.E. / Kahnt, J. / Ermler, U. / Shima, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 988.3 KB | Display | ![]() |
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PDB format | ![]() | 815.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 96.5 KB | Display | |
Data in CIF | ![]() | 139.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 61194.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: IN CHAIN A, D RESIDUE 261 IS A N1-METHYLHISTIDINE. RESIDUE 275 IS A C5-(S)-METHYLARGININE. RESIDUE 403 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 448 IS A THIOGLYCINE. Source: (natural) ![]() Plasmid details: DSMZ References: UniProt: A0A247D6X3*PLUS, coenzyme-B sulfoethylthiotransferase #2: Protein | Mass: 47362.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Plasmid details: DSMZ References: UniProt: A0A247D6X4*PLUS, coenzyme-B sulfoethylthiotransferase #3: Protein | Mass: 30368.537 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Plasmid details: DSMZ References: UniProt: A0A247D6X5*PLUS, coenzyme-B sulfoethylthiotransferase |
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-Non-polymers , 7 types, 1294 molecules ![](data/chem/img/TP7.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/K.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/K.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-K / | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-MG / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % / Description: Yellow brick |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 1 ul of MCR III from M. thermolithotrophicus with a concentration of 35 mg/ml was mixed with 1 ul of reservoir solution. Best crystals with a yellow brick morphology appeared after a few ...Details: 1 ul of MCR III from M. thermolithotrophicus with a concentration of 35 mg/ml was mixed with 1 ul of reservoir solution. Best crystals with a yellow brick morphology appeared after a few days in 19% (w/v) polyethylene glycol 3350 and 200 mM MgCl2 in the absence of buffer. The crystals were immersed in a solution containing 19% (w/v) PEG 3350 and 200 mM MgCl2, 30% glycerol (v/v) prior to freezing in liquid nitrogen. Temp details: grow between 290 - 293 Kelvin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.36 Å / Num. obs: 185011 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.92 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 26774 / CC1/2: 0.804 / Rpim(I) all: 0.346 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MCR III from Methanotorris formicicus Resolution: 1.9→45.63 Å / Cor.coef. Fo:Fc: 0.9567 / Cor.coef. Fo:Fc free: 0.9485 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.122
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Displacement parameters | Biso mean: 35.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.229 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→45.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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