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Yorodumi- PDB-6g3u: Structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, IDH -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g3u | ||||||
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Title | Structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, IDH | ||||||
Components | Isocitrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Isocitrate dehydrogenase / TCA cycle / metabolism / Pseudomonas aeruginosa | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.707 Å | ||||||
Authors | Crousilles, A. / Welch, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Gluconeogenic precursor availability regulates flux through the glyoxylate shunt inPseudomonas aeruginosa. Authors: Crousilles, A. / Dolan, S.K. / Brear, P. / Chirgadze, D.Y. / Welch, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g3u.cif.gz | 296.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g3u.ent.gz | 237 KB | Display | PDB format |
PDBx/mmJSON format | 6g3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/6g3u ftp://data.pdbj.org/pub/pdb/validation_reports/g3/6g3u | HTTPS FTP |
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-Related structure data
Related structure data | 5m2eC 6g1oC 4zdaS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 81249.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: idh, PA2624 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q9I0L4 #2: Chemical | ChemComp-NAP / | #3: Chemical | ChemComp-AKG / | #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: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, Sodium phosphate monobasic, glycerol, NADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.62 Å / Num. obs: 51799 / % possible obs: 98 % / Redundancy: 18.2 % / Biso Wilson estimate: 43.36 Å2 / Rrim(I) all: 0.176 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.7→2.78 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3682 / Rrim(I) all: 0.891 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZDA Resolution: 2.707→29.618 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 163.42 Å2 / Biso mean: 52.3057 Å2 / Biso min: 10.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.707→29.618 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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