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Yorodumi- PDB-2dht: Crystal structure of isocitrate dehydrogenase from Sulfolobus tok... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dht | ||||||
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Title | Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 | ||||||
Components | 409aa long hypothetical NADP-dependent isocitrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / homo dimer | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / tricarboxylic acid cycle / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kondo, H. / Murakami, M. / Ihara, K. / Suzuki, S. / Kouyama, T. | ||||||
Citation | Journal: To be Published Title: Crystal structure of isocitrate dehydrogenase of Sulfolobus tokodaii strain7 Authors: Kondo, H. / Murakami, M. / Ihara, K. / Suzuki, S. / Kouyama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dht.cif.gz | 167.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dht.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/2dht ftp://data.pdbj.org/pub/pdb/validation_reports/dh/2dht | HTTPS FTP |
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-Related structure data
Related structure data | 1v94S S: Starting model for refinement |
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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
#1: Protein | Mass: 46558.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Production host: Escherichia coli (E. coli) References: GenBank: 15623283, UniProt: Q96YK6*PLUS, isocitrate dehydrogenase (NADP+) #2: 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: 2.66 Å3/Da / Density % sol: 53.82 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 30, 2005 |
Radiation | Monochromator: double-crystal monochomator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→53.6 Å / Num. all: 33797 / Num. obs: 33300 / % possible obs: 97.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 3.2 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4511 / Rsym value: 0.492 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1v94 Resolution: 2.5→15 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 39.5232 Å2 / ksol: 0.333597 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.83 Å2 / Biso mean: 55.96 Å2 / Biso min: 20.26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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