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Yorodumi- PDB-5t3o: Crystal structure of the Phosphorybosylpyrophosphate synthetase I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t3o | ||||||
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Title | Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus | ||||||
Components | Ribose-phosphate pyrophosphokinase | ||||||
Keywords | TRANSFERASE / ModPipe Model of UP Q5SHU3 | ||||||
Function / homology | Function and homology information ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Timofeev, V.I. / Sinitsyna, E.V. / Abramchik, Y.A. / Kostromina, M.A. / Esipov, R.S. / Kuranova, I.P. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions. Authors: Timofeev, V.I. / Sinitsyna, E.V. / Kostromina, M.A. / Muravieva, T.I. / Makarov, D.A. / Mikheeva, O.O. / Kuranova, I.P. / Esipov, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t3o.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t3o.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t3o_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5t3o_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5t3o_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 5t3o_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/5t3o ftp://data.pdbj.org/pub/pdb/validation_reports/t3/5t3o | HTTPS FTP |
-Related structure data
Related structure data | 1dkrS 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: 33136.113 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: prs, TTHA1637 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SHU3, ribose-phosphate diphosphokinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: 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: 3.52 Å3/Da / Density % sol: 65.03 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / Details: 0.8M SA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→77.4 Å / Num. obs: 72677 / % possible obs: 99.97 % / Redundancy: 11.43 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 4.1075 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.55 % / Mean I/σ(I) obs: 2.01 / % possible all: 99.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DKR Resolution: 2.2→64.39 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.21 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.185 / 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: 47.097 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→64.39 Å
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Refine LS restraints |
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