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Yorodumi- PDB-4jis: Crystal structure of ribitol 5-phosphate cytidylyltransferase (Ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jis | ||||||
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Title | Crystal structure of ribitol 5-phosphate cytidylyltransferase (TarI) from Bacillus subtilis | ||||||
Components | ribitol-5-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / ribitol 5-phosphate cytidylyltransferase | ||||||
Function / homology | Function and homology information D-ribitol-5-phosphate cytidylyltransferase / D-ribitol-5-phosphate cytidylyltransferase activity / poly(ribitol phosphate) teichoic acid biosynthetic process / isoprenoid biosynthetic process / cell wall organization Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. spizizenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 Å | ||||||
Authors | Yang, C.S. / Chen, S.C. / Chen, Y.R. / Kuan, S.M. / Liu, Y.H. / Chen, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ribitol 5-phosphate cytidylyltransferase (TarI) from Bacillus subtilis Authors: Yang, C.S. / Chen, S.C. / Chen, Y.R. / Kuan, S.M. / Liu, Y.H. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jis.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jis.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/4jis ftp://data.pdbj.org/pub/pdb/validation_reports/ji/4jis | HTTPS FTP |
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-Related structure data
Related structure data | 3f1cS 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
#1: Protein | Mass: 28141.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria) Strain: w23 / Gene: BSUW23_17565, ispD, tarI / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8RKI9, D-ribitol-5-phosphate cytidylyltransferase #2: 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: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% PEG 6000, 0.1M MES-NaOH (pH 6.0), 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.772→30 Å / Num. all: 50947 / Num. obs: 49878 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.458 / Num. unique all: 4894 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F1C Resolution: 1.772→24.71 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8156 / SU ML: 0.18 / σ(F): 1.37 / Phase error: 25.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.25 Å2 / Biso mean: 38.96 Å2 / Biso min: 11.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.772→24.71 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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