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Yorodumi- PDB-1m6y: Crystal Structure Analysis of TM0872, a Putative SAM-dependent Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6y | ||||||
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Title | Crystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAH | ||||||
Components | S-adenosyl-methyltransferase mraW | ||||||
Keywords | TRANSFERASE / SAM-dependent Methyltransferase Fold / Protein-Cofactor Product Complex / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 16S rRNA (cytosine1402-N4)-methyltransferase / rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Miller, D.J. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain Authors: Miller, D.J. / Ouellette, N. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Anderson, W.F. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE BIOLOGICAL UNIT IS A TRIMER ACCORDING TO DYNAMIC LIGHT SCATTERING DATA. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m6y.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6y.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 1m6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6y ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35384.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0872 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZX6 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.79 Å3/Da / Density % sol: 55.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Drop: 50mM Na Cacodylate pH 6.5, 5mM HEPES pH 7.5, 0.1M Ammonium Sulfate, 9% PEG 8000, 0.25M NaCl, 1mM BME, 0.3mM S-adenosyl-L-homocysteine, 10mg/ml protein. Well: 0.1M Na Cacodylate pH 6.5, ...Details: Drop: 50mM Na Cacodylate pH 6.5, 5mM HEPES pH 7.5, 0.1M Ammonium Sulfate, 9% PEG 8000, 0.25M NaCl, 1mM BME, 0.3mM S-adenosyl-L-homocysteine, 10mg/ml protein. Well: 0.1M Na Cacodylate pH 6.5, 0.1M Ammonium Sulfate, 18 % PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9787, 0.9785, 0.9537 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 3, 2002 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→19.89 Å / Num. all: 62224 / Num. obs: 62185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.7 / Num. unique all: 6105 / % possible all: 99.7 | ||||||||||||
Reflection | *PLUS Num. obs: 62341 / Num. measured all: 854224 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3472061.43 / Data cutoff high rms absF: 3472061.43 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.5995 Å2 / ksol: 0.383992 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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