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- PDB-2o5w: Structure of the E. coli dihydroneopterin triphosphate pyrophosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o5w | ||||||
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Title | Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase in complex with Sm+3 and pyrophosphate | ||||||
![]() | dATP pyrophosphohydrolase | ||||||
![]() | HYDROLASE / dihydroneopterin triphosphate pyrophosphohydrolase nudix nucleoside triphosphate pyrophosphohydrolase mutt | ||||||
Function / homology | ![]() dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / dATP diphosphatase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gabelli, S.B. / Bianchet, M.A. / Amzel, L.M. | ||||||
![]() | ![]() Title: Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis. Authors: Gabelli, S.B. / Bianchet, M.A. / Xu, W. / Dunn, C.A. / Niu, Z.D. / Amzel, L.M. / Bessman, M.J. #1: Journal: J.Biol.Chem. / Year: 1996 Title: Escherichia coli orf17 codes for a nucleoside triphosphate pyrophosphohydrolase member of the mutt family of proteins Authors: O'Handley, S.F. / Frick, D.N. / Bullions, L.C. / Mildvan, A.S. / Bessman, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.4 KB | Display | ![]() |
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PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.1 KB | Display | ![]() |
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Full document | ![]() | 486.4 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17327.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AFC0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 5 types, 80 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/SM.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SM.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.3-1.5 AMMONIUM SULFATE, 1% PROPANOL, 3-5 MM DTT, 4MM SODIUM PYROPHOSPHATE, 100MM NA HEPES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.97 Å / Num. obs: 14304 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 |
Reflection shell | Resolution: 2.6→2.67 Å / Rsym value: 0.326 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 35.097 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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