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- PDB-5a0y: METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a0y | |||||||||
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Title | METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION | |||||||||
![]() | (METHYL-COENZYME M REDUCTASE I SUBUNIT ...![]() | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wagner, T. / Ermler, U. | |||||||||
![]() | ![]() Title: Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Authors: Wagner, T. / 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 | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 904.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5a8kC ![]() 5a8rC ![]() 5a8wC ![]() 3potS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-METHYL-COENZYME M REDUCTASE I SUBUNIT ... , 3 types, 6 molecules ADBECF
#1: Protein | ![]() Mass: 60637.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) Source: (natural) ![]() ![]() ![]() Strain: MARBURG References: UniProt: P11558, ![]() #2: Protein | ![]() Mass: 47279.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) Source: (natural) ![]() ![]() ![]() Strain: MARBURG References: UniProt: P11560, ![]() #3: Protein | ![]() Mass: 28797.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) Source: (natural) ![]() ![]() ![]() Strain: MARBURG References: UniProt: P11562, ![]() |
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-Non-polymers , 8 types, 2821 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F43.gif)
![](data/chem/img/COM.gif)
![](data/chem/img/TP7.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | ![]() #6: Chemical | #7: Chemical | ![]() #8: Chemical | ChemComp-K / | #9: Chemical | #10: Chemical | ![]() #11: Water | ChemComp-HOH / | ![]() |
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-Details
Nonpolymer details | DIDEHYDROASPARTATE (DYA): DIDEHYDROASPARTATE IS AN ASPARTATE CONTAINING A DOUBLE BOND BETWEEN THE C ...DIDEHYDROA |
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Sequence details | RESIDUE 450 IS A DIDEHYDROA |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % / Description: NONE |
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Crystal grow![]() | pH: 9 Details: 27.5% (V/V) PEG 400, 100 MM HEPES PH 7.5, 250 MM MGCL2, AND 200 MM NACL |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.1→48.35 Å / Num. obs: 937928 / % possible obs: 99.3 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Biso Wilson estimate: 9.06 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3POT Resolution: 1.1→48.346 Å / SU ML: 0.1 / σ(F): 1.33 / Phase error: 12.26 / Stereochemistry target values: ML Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODEL A NEW POST-TRANSLATIONAL MODIFICATION IS PRESENT IN THE CHAIN A AND D CALLED DIDEHYDROASPARTATE AT THE POSITION 450
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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 mean: 15.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→48.346 Å
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Refine LS restraints |
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LS refinement shell |
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