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Yorodumi- PDB-5t6b: X-ray structure of the KijD1 C3-methyltransfeerase, converted to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t6b | ||||||
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Title | X-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form | ||||||
Components | Sugar 3-C-methyl transferase | ||||||
Keywords | TRANSFERASE / methyltransferase / antitumor / antibiotic / kijanimicin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Actinomadura kijaniata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. / Dow, G.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2016 Title: Structural studies on KijD1, a sugar C-3'-methyltransferase. Authors: Dow, G.T. / 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 | 5t6b.cif.gz | 339.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t6b.ent.gz | 272.1 KB | Display | PDB format |
PDBx/mmJSON format | 5t6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/5t6b ftp://data.pdbj.org/pub/pdb/validation_reports/t6/5t6b | HTTPS FTP |
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-Related structure data
Related structure data | 5t64SC 5t67C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45983.754 Da / Num. of mol.: 4 Mutation: K92M, Q95R, R96D, L97F, A105P, D388E, R398H, R412H, V413I, L414R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura kijaniata (bacteria) / Gene: KijD1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B3TMQ9 |
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-Non-polymers , 5 types, 751 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAH / #4: Chemical | #5: Chemical | ChemComp-TMP / #6: 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: 1.94 Å3/Da / Density % sol: 36.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 18-22% PEG-3350, 2%MPD, 100 mM MES, 10 mM TDP, 5 mM SAH |
-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: Dec 12, 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→75 Å / Num. obs: 90291 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.074 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.1 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T64 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.861 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.191 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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