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Open data
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Basic information
Entry | Database: PDB / ID: 4lrd | ||||||
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Title | Phosphopentomutase 4H11 variant | ||||||
![]() | Phosphopentomutase 4H11 variant | ||||||
![]() | 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 | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
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Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lr7C ![]() 4lr8C ![]() 4lr9C ![]() 4lraC ![]() 4lrbC ![]() 4lrcC ![]() 4lreC ![]() 4lrfC ![]() 3m8zS S: Starting model for refinement C: citing same article ( |
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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: 46504.441 Da / Num. of mol.: 1 / Mutation: V158L/T81I/M190K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.45 Details: 20 mg/mL protein in 1 mM manganese chloride, 25 mM Tris-HCl, pH 7.4 against a reservoir of 25% PEG3350, 50 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.45, 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 / Date: Jun 20, 2013 |
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: 1.78→50 Å / Num. obs: 34906 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Rsym value: 0.073 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.78→1.81 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.253 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3M8Z Resolution: 1.78→39.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.007 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / 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: 14.063 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→39.02 Å
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Refine LS restraints |
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