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Yorodumi- PDB-6mro: Crystal structure of methyl transferase from Methanosarcina aceti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mro | ||||||
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Title | Crystal structure of methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution, Northeast Structural Genomics Consortium (NESG) Target MvR53. | ||||||
Components | methyl transferase from Methanosarcina acetivoransMethyltransferase | ||||||
Keywords | TRANSFERASE / methyl transferase / SAH / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanosarcina acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Singh, S. / Forouhar, F. / Wang, C. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution. Authors: Singh, S. / Forouhar, F. / Wang, C. / Vorobiev, S.M. / Neky, M.J. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mro.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mro.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/6mro ftp://data.pdbj.org/pub/pdb/validation_reports/mr/6mro | HTTPS FTP |
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-Related structure data
Related structure data | 4necS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21992.178 Da / Num. of mol.: 1 / Mutation: D65R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea) Strain: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Gene: MA_2137 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TNZ0 | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.66 % |
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Crystal grow | Temperature: 293.15 K / Method: microbatch / pH: 7 Details: 0.2M Calcium chloride dihydrate 0.1M MES 6.0 20% w/v PEG-6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.99 Å / Num. obs: 22761 / % possible obs: 99.59 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09546 / Rpim(I) all: 0.03797 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.458 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2267 / CC1/2: 0.493 / Rpim(I) all: 0.6174 / % possible all: 99.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NEC Resolution: 1.6→40.99 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.8004 Å / Origin y: -5.213 Å / Origin z: -0.9919 Å
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Refinement TLS group | Selection details: all |