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Open data
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Basic information
Entry | Database: PDB / ID: 4lre | |||||||||
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Title | Phosphopentomutase soaked with 2,3-dideoxyribose 5-phosphate | |||||||||
![]() | Phosphopentomutase | |||||||||
![]() | ISOMERASE / alkaline phosphatase family | |||||||||
Function / homology | ![]() phosphopentomutase / phosphopentomutase activity / cellular metabolic compound salvage / 5-phosphoribose 1-diphosphate biosynthetic process / deoxyribonucleotide catabolic process / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Birmingham, W.A. / Starbird, C.A. / Panosian, T.D. / Nannemann, D.P. / Iverson, T.M. / Bachmann, B.O. | |||||||||
![]() | ![]() Title: Bioretrosynthetic construction of a didanosine biosynthetic pathway. Authors: Birmingham, W.R. / Starbird, C.A. / Panosian, T.D. / Nannemann, D.P. / Iverson, T.M. / Bachmann, B.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.9 KB | Display | ![]() |
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PDB format | ![]() | 200.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lr7C ![]() 4lr8C ![]() 4lr9C ![]() 4lraC ![]() 4lrbC ![]() 4lrcC ![]() 4lrdC ![]() 4lrfC ![]() 3m8wS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46480.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Sugar | ChemComp-1X4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 13% PEG3350, 50 mM manganese chloride, 75 mM ammonium acetate, 100 mM Bis-Tris, crystals soaked in reservoir solution + 10 mM dideoxyribose 5-phosphate for 30 minutes, pH 5.5, VAPOR ...Details: 13% PEG3350, 50 mM manganese chloride, 75 mM ammonium acetate, 100 mM Bis-Tris, crystals soaked in reservoir solution + 10 mM dideoxyribose 5-phosphate for 30 minutes, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 79568 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Rsym value: 0.083 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.283 / % possible all: 88.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3M8W Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.372 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.991 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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