+Open data
-Basic information
Entry | Database: PDB / ID: 4lrf | |||||||||
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Title | Phosphopentomutase S154G variant soaked with ribose 5-phosphate | |||||||||
Components | Phosphopentomutase | |||||||||
Keywords | ISOMERASE / alkaline phosphatase family | |||||||||
Function / homology | Function and homology information 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 | Bacillus cereus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Birmingham, W.A. / Starbird, C.A. / Panosian, T.D. / Nannemann, D.P. / Iverson, T.M. / Bachmann, B.O. | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lrf.cif.gz | 486.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lrf.ent.gz | 397.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lrf_validation.pdf.gz | 482.3 KB | Display | wwPDB validaton report |
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Full document | 4lrf_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 4lrf_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 4lrf_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/4lrf ftp://data.pdbj.org/pub/pdb/validation_reports/lr/4lrf | HTTPS FTP |
-Related structure data
Related structure data | 4lr7C 4lr8C 4lr9C 4lraC 4lrbC 4lrcC 4lrdC 4lreC 3m8wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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.) Bacillus cereus (bacteria) / Gene: BC_4087, deoB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q818Z9, phosphopentomutase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Sugar | #5: 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: 2.55 Å3/Da / Density % sol: 51.78 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å |
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→50 Å / Num. obs: 94933 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Rsym value: 0.087 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.386 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3M8W Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.013 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / 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: 22.724 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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