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Yorodumi- PDB-6ajb: Crystal structure of Trypanosoma brucei glycosomal isocitrate deh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ajb | ||||||
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Title | Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and ca2+ | ||||||
Components | Isocitrate dehydrogenase [NADP] | ||||||
Keywords | OXIDOREDUCTASE / Trypanosoma brucei / glycosome / metabolism / isocitrate dehydrogenase | ||||||
Function / homology | Function and homology information isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / glycosome / tricarboxylic acid cycle / NAD binding / magnesium ion binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. ...Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K. | ||||||
Citation | Journal: To Be Published Title: Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+) Authors: Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ajb.cif.gz | 649.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ajb.ent.gz | 544.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ajb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ajb_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6ajb_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6ajb_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 6ajb_validation.cif.gz | 78.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/6ajb ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6ajb | HTTPS FTP |
-Related structure data
Related structure data | 6aj6SC 6aj8C 6ajaC 6ajcC 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
#1: Protein | Mass: 46791.590 Da / Num. of mol.: 4 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: ILtat 1.4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) References: UniProt: Q387G0, isocitrate dehydrogenase (NADP+) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-AKG / | Sequence details | The sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference ...The sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference available at uniprot at the time of data processing was derived from a different strain TRYPANOSOM | |
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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: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 6000, 100 mM HEPES/NaOH pH 7.0, 200mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 39505 / % possible obs: 93.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1842 / % possible all: 89.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AJ6 Resolution: 2.9→19.98 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.839 / SU B: 57.731 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / 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: 56.642 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→19.98 Å
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Refine LS restraints |
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