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- PDB-5dan: Crystal structure of a novel aldo keto reductase Tm1743 from Ther... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dan | ||||||||||||
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Title | Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+ | ||||||||||||
![]() | 2,5-diketo-D-gluconic acid reductase | ||||||||||||
![]() | OXIDOREDUCTASE / Aldo keto reductase / Thermostable / NADP | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Xu, X. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+ Authors: Xu, X. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.3 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.9 KB | Display | ![]() |
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Full document | ![]() | 738.5 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pyfS S: Starting model for refinement |
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Similar structure data |
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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: 31402.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: gene synthesis Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1743, Tmari_1751 / Plasmid: pET-28a(+) / Details (production host): N His6 tag / Production host: ![]() ![]() References: UniProt: Q9X265, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M Calcium chloride dehydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20 % v/v 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 25576 / % possible obs: 95.8 % / Redundancy: 10 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 3.3 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PYF Resolution: 2→42.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.229 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.81 Å2 / Biso mean: 35.755 Å2 / Biso min: 20.27 Å2
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Refinement step | Cycle: final / Resolution: 2→42.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.004→2.056 Å / Total num. of bins used: 20
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