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Yorodumi- PDB-6hje: Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hje | ||||||
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Title | Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27 | ||||||
Components | Proline racemase A | ||||||
Keywords | ISOMERASE / Proline Racemase / Drug Design / Michael Reaction | ||||||
Function / homology | Function and homology information proline racemase activity / proline racemase / 4-hydroxyproline epimerase activity / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Saul, F. / Haouz, A. / Uriac, P. / Blondel, A. / Minoprio, P. | ||||||
Funding support | France, 1items
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Citation | Journal: PLoS Negl Trop Dis / Year: 2018 Title: Designed mono- and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography. Authors: Amaral, P.A. / Autheman, D. / de Melo, G.D. / Gouault, N. / Cupif, J.F. / Goyard, S. / Dutra, P. / Coatnoan, N. / Cosson, A. / Monet, D. / Saul, F. / Haouz, A. / Uriac, P. / Blondel, A. / Minoprio, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hje.cif.gz | 157.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hje.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 6hje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hje_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6hje_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6hje_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 6hje_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/6hje ftp://data.pdbj.org/pub/pdb/validation_reports/hj/6hje | HTTPS FTP |
-Related structure data
Related structure data | 6hjfC 6hjgC 1w61S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45796.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: PA45-A, Tc00.1047053506795.80 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DA80, proline racemase #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M POTASSIUM PHOSPHATE DIBASIC 21% (W/V) PEG-3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.00637 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00637 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.3 Å / Num. obs: 54731 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.7 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W61 Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.357 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.164 / 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: 49.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45 Å
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Refine LS restraints |
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