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Open data
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Basic information
Entry | Database: PDB / ID: 4lra | ||||||
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Title | Phosphopentomutase S154G variant | ||||||
![]() | 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 | ![]() | 483.3 KB | Display | ![]() |
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PDB format | ![]() | 396.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.3 KB | Display | ![]() |
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Full document | ![]() | 473.5 KB | Display | |
Data in XML | ![]() | 49.9 KB | Display | |
Data in CIF | ![]() | 72.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lr7C ![]() 4lr8C ![]() 4lr9C ![]() 4lrbC ![]() 4lrcC ![]() 4lrdC ![]() 4lreC ![]() 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: 46450.348 Da / Num. of mol.: 3 / Mutation: S154G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG3350, 50 mM manganese chloride, 50 mM ammonium acetate, 100 mM Bis-Tris, 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: 1.95→50 Å / Num. obs: 98816 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Rsym value: 0.075 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.95→1.98 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.376 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3M8W Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.812 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.145 / 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: 36.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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