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Yorodumi- PDB-5fad: SAH complex with aKMT from the hyperthermophilic archaeon Sulfolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fad | ||||||
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Title | SAH complex with aKMT from the hyperthermophilic archaeon Sulfolobus islandicus | ||||||
Components | Ribosomal protein L11 methyltransferase, putativeRibosome | ||||||
Keywords | TRANSFERASE / protein methyltransferase | ||||||
Function / homology | Function and homology information protein-lysine N-methyltransferase activity / methylation / ribosome / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus islandicus (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Ouyang, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol.Cell Proteomics / Year: 2016 Title: aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism Authors: Chu, Y. / Zhu, Y. / Chen, Y. / Li, W. / Zhang, Z. / Liu, D. / Wang, T. / Ma, J. / Deng, H. / Liu, Z.J. / Ouyang, S. / Huang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fad.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fad.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/5fad ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fad | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18179.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus (strain M.14.25 / Kamchatka #1) (acidophilic) Strain: M.14.25 / Kamchatka #1 / Gene: M1425_1574 / Production host: Escherichia coli (E. coli) / References: UniProt: C3MWA1 |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 10M nickel chloride, 0.1M Tris-HCl, pH 8.5, 20%(w/v) PEG 2,000 MME |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→35.9 Å / Num. obs: 11289 / % possible obs: 93.7 % / Redundancy: 3.3 % / Net I/σ(I): 33.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→35.898 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→35.898 Å
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Refine LS restraints |
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LS refinement shell |
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