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Yorodumi- PDB-6gxq: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gxq | ||||||
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Title | Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1335 | ||||||
Components | Phosphodiesterase | ||||||
Keywords | HYDROLASE / Parasitic phosphodiesterase / African trypanosomiasis / sleeping sickness | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cell morphogenesis / signal transduction / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Singh, A.K. / Brown, D.G. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2019 Title: Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2). Authors: de Heuvel, E. / Singh, A.K. / Boronat, P. / Kooistra, A.J. / van der Meer, T. / Sadek, P. / Blaazer, A.R. / Shaner, N.C. / Bindels, D.S. / Caljon, G. / Maes, L. / Sterk, G.J. / Siderius, M. ...Authors: de Heuvel, E. / Singh, A.K. / Boronat, P. / Kooistra, A.J. / van der Meer, T. / Sadek, P. / Blaazer, A.R. / Shaner, N.C. / Bindels, D.S. / Caljon, G. / Maes, L. / Sterk, G.J. / Siderius, M. / Oberholzer, M. / de Esch, I.J.P. / Brown, D.G. / Leurs, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gxq.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gxq.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/6gxq ftp://data.pdbj.org/pub/pdb/validation_reports/gx/6gxq | HTTPS FTP |
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-Related structure data
Related structure data | 6hwoC 6rb6C 6rcwC 6rfnC 6rfwC 6rgkC 4i15S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 586 - 916 / Label seq-ID: 28 - 358
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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.) Trypanosoma brucei (eukaryote) / Gene: PDEB1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Non-polymers , 6 types, 446 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GAI / #5: Chemical | ChemComp-FFZ / | #6: Chemical | #7: 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: 2.63 Å3/Da / Density % sol: 53.21 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→64.76 Å / Num. obs: 59811 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.063 / Rrim(I) all: 0.117 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4410 / CC1/2: 0.595 / Rpim(I) all: 0.45 / Rrim(I) all: 0.838 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I15 Resolution: 1.96→57.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.204 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.158 / 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: 40.075 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→57.28 Å
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Refine LS restraints |
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