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- PDB-5vug: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vug | ||||||
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Title | Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase Domain of Uncharacterized Protein Rv2277c from Mycobacterium tuberculosis | ||||||
![]() | Uncharacterized protein Rv2277c | ||||||
![]() | Structural genomics / Unknown function / alpha-beta fold / TIM barrel / glycerophosphodiester phosphodiesterase domain / MCSG / PSI-Biology / Midwest Center for Structural Genomics | ||||||
Function / homology | Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / Uncharacterized protein Rv2277c![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase Domain of Uncharacterized Protein Rv2277c from Mycobacterium tuberculosis Authors: Kim, Y. / Li, H. / Endres, M. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.6 KB | Display | ![]() |
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PDB format | ![]() | 95.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 431.4 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30530.209 Da / Num. of mol.: 1 / Fragment: residues 24-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: Rv2277c, MTCY339.33 / Plasmid: pMCSG68 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Calcium Acetate, 0.1 M Imidazole:HCl pH 8.0, 10% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 55320 / % possible obs: 98.3 % / Redundancy: 6.3 % / Rsym value: 0.094 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1974 / CC1/2: 0.69 / Rsym value: 0.61 / % possible all: 71.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→26.275 Å
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Refine LS restraints |
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LS refinement shell |
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