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Yorodumi- PDB-2pu8: Structures of 5-methylthioribose kinase reveal substrate specific... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pu8 | ||||||
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Title | Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding | ||||||
Components | Methylthioribose kinase | ||||||
Keywords | TRANSFERASE / 5-methylthioribose kinase / methionine recycling pathway | ||||||
Function / homology | Function and homology information S-methyl-5-thioribose kinase / S-methyl-5-thioribose kinase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Ku, S.-Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding Authors: Ku, S.-Y. / Yip, P. / Cornell, K.A. / Riscoe, M.K. / Behr, J.-B. / Guillerm, G. / Howell, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pu8.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pu8.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/2pu8 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/2pu8 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3 / Auth seq-ID: 7 - 396 / Label seq-ID: 7 - 396
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-Components
#1: Protein | Mass: 45139.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mtnK, ykrT / Plasmid: pTRCHis2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O31663, S-methyl-5-thioribose kinase #2: Chemical | ChemComp-CPS / | #3: 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: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 2000MME, 0.3M sodium acetate, 0.1M TrisHCl, 8mM CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 18, 2005 / Details: Osmic optics |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→107.2 Å / Num. all: 54913 / Num. obs: 53540 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.1→2.154 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 6.2 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→65.68 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.779 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.192 / 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: 29.387 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→65.68 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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