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- PDB-3pot: Structural analysis of a Ni(III)-methyl species in methyl-coenzym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pot | ||||||
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Title | Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis | ||||||
![]() | (Methyl-coenzyme M reductase I subunit ...) x 3 | ||||||
![]() | TRANSFERASE / METAL-BINDING / NICKEL / METHYL-COENZYME M REDUCTASE / 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. / Wilmot, C.M. | ||||||
![]() | ![]() Title: Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis. Authors: Cedervall, P.E. / Dey, M. / Li, X. / Sarangi, R. / Hedman, B. / 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 | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 851.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 113.8 KB | Display | |
Data in CIF | ![]() | 172.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m2rS S: Starting model for refinement |
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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
-Methyl-coenzyme M reductase I subunit ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 60639.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase #2: Protein | Mass: 47279.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase #3: Protein | Mass: 28797.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase |
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-Non-polymers , 9 types, 2626 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/TXZ.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/06C.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/TXZ.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/06C.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-K / | #11: Chemical | ChemComp-EDO / | #12: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 06C HAS REACTED WITH THE ENZYME METAL CENTER TO YIELD A NI-BOUND METHYL GROUP (CH3) (THE NI IS PART ...06C HAS REACTED WITH THE ENZYME METAL CENTER TO YIELD A NI-BOUND METHYL GROUP (CH3) (THE NI IS PART OF COFACTOR F430) AND AN IODIDE (I-) THAT IS SITUATED IN THE ACTIVE SITE AT A DISTANCE OF 4 ANGSTROM FROM CH3 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Hepes-Na pH 7.5, 150 mM magnesium acetate and 20% PEG 400., VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2009 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 721334 / Num. obs: 721334 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 13.27 Å2 / Rsym value: 0.075 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 72029 / Rsym value: 0.43 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID: 3M2R, but with all waters, coenzymes and metal ions removed Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.05 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 12.192 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1779 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.232 Å / Total num. of bins used: 20
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