+Open data
-Basic information
Entry | Database: PDB / ID: 6gxg | ||||||
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Title | Tryparedoxin from Trypanosoma brucei in complex with CFT | ||||||
Components | (Tryparedoxin) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Covalent Inhibitor / Photoreduction / Inhibitor-Induced Dimerization / Monomer-Dimer Mixture | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Bader, N. / Wagner, A. / Hellmich, U. / Schindelin, H. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2019 Title: Inhibitor-Induced Dimerization of an Essential Oxidoreductase from African Trypanosomes. Authors: Wagner, A. / Le, T.A. / Brennich, M. / Klein, P. / Bader, N. / Diehl, E. / Paszek, D. / Weickhmann, A.K. / Dirdjaja, N. / Krauth-Siegel, R.L. / Engels, B. / Opatz, T. / Schindelin, H. / Hellmich, U.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gxg.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gxg.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 6gxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/6gxg ftp://data.pdbj.org/pub/pdb/validation_reports/gx/6gxg | HTTPS FTP |
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-Related structure data
Related structure data | 6gxyC 1o73S 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15878.901 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: O77404 | ||||||
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#2: Protein | Mass: 16090.119 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: O77404 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.045 M Na-citrate; 100 mM Na-acetate buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 45750 / % possible obs: 97.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.056 / Rrim(I) all: 0.146 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.441 / Num. unique obs: 2210 / CC1/2: 0.6 / Rpim(I) all: 0.577 / Rrim(I) all: 1.554 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1o73 Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.017 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / 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: 22.262 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→20 Å
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Refine LS restraints |
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