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- PDB-6m3s: Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m3s | ||||||
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Title | Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004 | ||||||
![]() | Isocitrate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / isocitrate dehydrogenase / CARBOHYDRATE | ||||||
Function / homology | ![]() isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / NAD binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, G.P. | ||||||
![]() | ![]() Title: Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004 Authors: Zhu, G.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148 KB | Display | ![]() |
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PDB format | ![]() | 113.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ltfC ![]() 5grhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36533.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A2S4JWD6, isocitrate dehydrogenase (NAD+) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, 4 mM DL-Isocitrate, 4 mM NAD, 2 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 34265 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 37.13 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.058 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.44 / Num. unique obs: 1733 / R split: 0.21 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GRH Resolution: 2.3→48.33 Å / SU ML: 0.2459 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.5784
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.33 Å
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Refine LS restraints |
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LS refinement shell |
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