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- PDB-3m2u: Structural Insight into Methyl-Coenzyme M Reductase Chemistry usi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m2u | ||||||
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Title | Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues | ||||||
![]() | (Methyl-coenzyme M reductase I subunit ...) x 3 | ||||||
![]() | TRANSFERASE / Methyl-Coenzyme M Reductase / Nickel / Metal-binding / Methanogenesis / Methylation | ||||||
Function / homology | ![]() coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cedervall, P.E. / Dey, M. / Ragsdale, S.W. / Wilmot, C.M. | ||||||
![]() | ![]() Title: Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues. Authors: Cedervall, P.E. / Dey, M. / Pearson, A.R. / Ragsdale, S.W. / Wilmot, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 561 KB | Display | ![]() |
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PDB format | ![]() | 466.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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 I subunit ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 60508.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: Marburg / DSM 2133 References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase #2: Protein | Mass: 47148.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: Marburg / DSM 2133 References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase #3: Protein | Mass: 28666.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: Marburg / DSM 2133 References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase |
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-Non-polymers , 10 types, 2321 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/TXZ.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/TXZ.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-EDO / #11: Chemical | #12: Chemical | ChemComp-ZN / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop Details: PEG 400, magnesium acetate, vapor diffusion, sitting drop, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2007 |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 446793 / Num. obs: 446253 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.389 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 4.029 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Total num. of bins used: 20
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