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Open data
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Basic information
Entry | Database: PDB / ID: 2ekq | ||||||
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Title | Structure of TT0495 protein from Thermus thermophilus | ||||||
![]() | 2-deoxy-D-gluconate 3-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / gluconate dehydrogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lokanath, N.K. / Pampa, K.J. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8 Authors: Pampa, K.J. / Lokanath, N.K. / Kunishima, N. / Rai, R.V. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.2 KB | Display | ![]() |
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PDB format | ![]() | 166.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.6 KB | Display | ![]() |
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Full document | ![]() | 482 KB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 69.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ekpC ![]() 4jp2C ![]() 4jp3C ![]() 1x1eS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25702.729 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q53W82, 2-deoxy-D-gluconate 3-dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.4 Details: 22% PEG 2000, 0.3M NH2SO4, pH 9.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 13, 2006 / Details: graphite |
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: 1.8→40 Å / Num. all: 114641 / Num. obs: 114536 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X1E Resolution: 1.8→32.49 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→32.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å |