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Open data
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Basic information
Entry | Database: PDB / ID: 5gl3 | ||||||
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Title | Crystal structure of TON_0340 in complex with Mg | ||||||
![]() | Uncharacterized protein | ||||||
![]() | UNKNOWN FUNCTION / TON_0340 / Thermococcus onnurineus / Mn2+-dependent phosphatase | ||||||
Function / homology | ![]() D-glutamate cyclase activity / glutamate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S.G. / Sohn, Y.S. / Oh, B.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase. Authors: Sohn, Y.S. / Lee, S.G. / Lee, K.H. / Ku, B. / Shin, H.C. / Cha, S.S. / Kim, Y.G. / Lee, H.S. / Kang, S.G. / Oh, B.H. #1: ![]() Title: Experimental phasing using zinc anomalous scattering. Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Kim, M.K. / Lee, S.G. / Lee, K.H. / Oh, B.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 307 KB | Display | ![]() |
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PDB format | ![]() | 251.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.9 KB | Display | ![]() |
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Full document | ![]() | 527.8 KB | Display | |
Data in XML | ![]() | 62.2 KB | Display | |
Data in CIF | ![]() | 84.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gkxC ![]() 5gl2C ![]() 5gl4C ![]() 4fc5S 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29107.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: sodium acetate pH, 16% 2-methyl-2,4-pentanediol,magnesium acetate |
-Data collection
Diffraction | Mean temperature: 295 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 73586 / % possible obs: 87.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.061 / Χ2: 2.114 / Net I/av σ(I): 31.136 / Net I/σ(I): 16.2 / Num. measured all: 423552 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FC5 Resolution: 2.4→50 Å / Cross valid method: FREE R-VALUE / σ(F): 30
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Solvent computation | Bsol: 28.9921 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 100.91 Å2 / Biso mean: 43.3875 Å2 / Biso min: 15.67 Å2
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Refinement step | Cycle: final / Resolution: 2.4→50 Å
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Refine LS restraints |
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Xplor file |
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