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Yorodumi- PDB-5g0r: METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g0r | |||||||||
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Title | METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENSIS EXPOSED TO 3-NITROOXYPROPANOL | |||||||||
Components | (METHYL-COENZYME M REDUCTASE I SUBUNIT ...) x 3 | |||||||||
Keywords | TRANSFERASE / METHYL-COENZYMEM / METHYL-COENZYMEM REDUCTASE EXPOSED TO 3-NITROOXYPROPANOL / POSTTRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOBACTERIUM / NICKEL / OXIDATION-REDUCTION / OXDOREDUCTASES / PHOSPHOTHREONINE / THIOGLYCINE / 3- NITROOXYPROPANOL / INHIBITOR / GREENHOUSE GAS | |||||||||
Function / homology | Function and homology information coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | METHANOTHERMOBACTER MARBURGENSIS (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Wagner, T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Mode of Action Uncovered for the Specific Reduction of Methane Emissions from Ruminants by the Small Molecule 3-Nitrooxypropanol. Authors: Duin, E.C. / Wagner, T. / Shima, S. / Prakash, D. / Cronin, B. / Yanez-Ruiz, D.R. / Duval, S. / Rumbeli, R. / Stemmler, R.T. / Thauer, R.K. / Kindermann, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g0r.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5g0r.ent.gz | 846.9 KB | Display | PDB format |
PDBx/mmJSON format | 5g0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g0r_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5g0r_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5g0r_validation.xml.gz | 111.8 KB | Display | |
Data in CIF | 5g0r_validation.cif.gz | 171.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g0r ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g0r | HTTPS FTP |
-Related structure data
Related structure data | 5a0yS S: Starting model for refinement |
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Similar structure data |
-Links
-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) METHANOTHERMOBACTER MARBURGENSIS (archaea) Strain: MARBURG References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase #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) METHANOTHERMOBACTER MARBURGENSIS (archaea) Strain: MARBURG References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase #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) METHANOTHERMOBACTER MARBURGENSIS (archaea) Strain: MARBURG References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase |
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-Non-polymers , 7 types, 2638 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-K / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE 450 IS A DIDEHYDROA |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 25-28 % V/V PEG 400, 300 MM MGCL2, 200 MM NACL AND 100 MM HEPES PH 7.5 CRYSTAL GROWTH AT 8 DEGREE CELSIUS UNDER AEROBIC CONDITION |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97128 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97128 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→38.79 Å / Num. obs: 633330 / % possible obs: 98.5 % / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Biso Wilson estimate: 9.86 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A0Y Resolution: 1.25→38.795 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 10.8 / Stereochemistry target values: ML Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODE THE INHIBITOR 3-NITROOXYPROPANOL HAS POSSIBLY REDUCED THE NICKEL CENTER AND IS NOW HYDROLYSED IN THE ...Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODE THE INHIBITOR 3-NITROOXYPROPANOL HAS POSSIBLY REDUCED THE NICKEL CENTER AND IS NOW HYDROLYSED IN THE ACTIVE SITE. SINCE THERE IS A LOW PARTIAL OCCUPANCY OF THE BROKEN COMPOUND (NITRITE AND 1-3-PROPANEDIOL) IN THE ACTIVE SITE, WATER MOLECULE HAVE BEEN PLACED INSTEAD.
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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: 15.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→38.795 Å
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Refine LS restraints |
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LS refinement shell |
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