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Yorodumi- PDB-2e0c: crystal structure of isocitrate dehydrogenase from Sulfolobus tok... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e0c | ||||||
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Title | crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 at 2.0 A resolution | ||||||
Components | 409aa long hypothetical NADP-dependent isocitrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / homedimer | ||||||
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 str. 7 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kouyama, T. | ||||||
Citation | Journal: Archaea / Year: 2018 Title: Crystal Structures of the Putative Isocitrate Dehydrogenase fromSulfolobus tokodaiiStrain 7 in the Apo and NADP+-Bound Forms. Authors: Kondo, H. / Murakami, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e0c.cif.gz | 175.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e0c.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e0c_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 2e0c_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 2e0c_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 2e0c_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/2e0c ftp://data.pdbj.org/pub/pdb/validation_reports/e0/2e0c | HTTPS FTP |
-Related structure data
Related structure data | 2e5mC 2dhtS 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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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 str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: strain 7 / Production host: Escherichia coli (E. coli) References: UniProt: Q96YK6, 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: 2.67 Å3/Da / Density % sol: 53.91 % |
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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: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 66041 / Num. obs: 65823 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9631 / Rsym value: 0.413 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dht Resolution: 2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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