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- PDB-6ftm: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ftm | ||||||
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Title | Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048 | ||||||
![]() | Phosphodiesterase | ||||||
![]() | HYDROLASE / Parasitic phosphodiesterase / African trypanosomiasis / sleeping sickness | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cGMP catabolic process / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / cell morphogenesis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, A.K. / Brown, D.G. | ||||||
![]() | ![]() Title: Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048 Authors: de Heuvel, E. / Singh, A.K. / Brown, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.3 KB | Display | ![]() |
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PDB format | ![]() | 123.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i15S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40623.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residues 565-918 / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Non-polymers , 7 types, 367 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GAI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/E6Z.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GAI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/E6Z.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GAI / #6: Chemical | ChemComp-FMT / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→70.28 Å / Num. obs: 58838 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.069 / Rrim(I) all: 0.125 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4554 / CC1/2: 0.603 / Rpim(I) all: 0.343 / Rrim(I) all: 0.589 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I15 Resolution: 2.1→70.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.945 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.136 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.055 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→70.28 Å
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Refine LS restraints |
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