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Yorodumi- PDB-6fdw: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fdw | ||||||
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Title | Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356 | ||||||
Components | Phosphodiesterase | ||||||
Keywords | HYDROLASE / Parasitic phosphodiesterase / African trypanosomiasis / sleeping sickness | ||||||
Function / homology | Function and homology information 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 | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Singh, A.K. / Brown, D.G. | ||||||
Citation | Journal: To be published Title: TbrPDEB1 structure with inhibitor NPD-356 Authors: Salado, I.G. / Moreno, C. / Sakaine, G. / Singh, A.K. / Blaazer, A.R. / Siderius, M. / Matheeussen, A. / Gul, S. / Maes, L. / Leurs, R. / Brown, D.G. / Augustyns, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fdw.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fdw.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fdw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6fdw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6fdw_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 6fdw_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fdw ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fdw | HTTPS FTP |
-Related structure data
Related structure data | 4i15S S: Starting model for refinement |
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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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-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) References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Non-polymers , 6 types, 240 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GAI / | #6: Chemical | ChemComp-GOL / | #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: 2.65 Å3/Da / Density % sol: 53.56 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2017 / Details: CRL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→33.91 Å / Num. obs: 60184 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4487 / CC1/2: 0.604 / Rpim(I) all: 0.589 / Rrim(I) all: 1.11 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I15 Resolution: 1.96→33.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.708 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.148 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U values refined individually
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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: 52.319 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→33.91 Å
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Refine LS restraints |
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