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Yorodumi- PDB-5bsz: X-ray structure of the sugar N-methyltransferase KedS8 from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bsz | ||||||
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Title | X-ray structure of the sugar N-methyltransferase KedS8 from Streptoalloteichus sp ATCC 53650 | ||||||
Components | N-methyltransferase | ||||||
Keywords | TRANSFERASE / N-methyltransferase kedarcidin trideoxysugar S-adenosylmethionine | ||||||
Function / homology | Methyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / THYMIDINE / N-methyltransferase Function and homology information | ||||||
Biological species | Streptoalloteichus sp. ATCC 53650 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Thoden, J.B. / Delvaux, N.A. / Holden, H.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Molecular architecture of KedS8, a sugar N-methyltransferase from Streptoalloteichus sp. ATCC 53650. Authors: Delvaux, N.A. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bsz.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bsz.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/5bsz ftp://data.pdbj.org/pub/pdb/validation_reports/bs/5bsz | HTTPS FTP |
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-Related structure data
Related structure data | 3bxoS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27114.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptoalloteichus sp. ATCC 53650 (bacteria) Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: K4P132 | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-THM / | #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: 3 Å3/Da / Density % sol: 58.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 28-33% MPD, 2.5 mM SAH, 100 mM MOPS / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 21803 / Num. obs: 21803 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.2 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3bxo Resolution: 2→28.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.117 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.149 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.478 Å2
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Refinement step | Cycle: 1 / Resolution: 2→28.71 Å
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