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- PDB-6ytz: Crystal structure of Malus domestica Double Bond Reductase (MdDBR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ytz | ||||||
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Title | Crystal structure of Malus domestica Double Bond Reductase (MdDBR) in complex with NADPH | ||||||
![]() | Double Bond Reductase | ||||||
![]() | BIOSYNTHETIC PROTEIN / phenylpropanoid pathway / double bond reductase / Malus domestica | ||||||
Function / homology | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / R-1,2-PROPANEDIOL![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Caliandro, R. / Polsinelli, I. / Demitri, N. / Benini, S. | ||||||
![]() | ![]() Title: The structural and functional characterization of Malus domestica double bond reductase MdDBR provides insights towards the identification of its substrates. Authors: Caliandro, R. / Polsinelli, I. / Demitri, N. / Musiani, F. / Martens, S. / Benini, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 129.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 748.4 KB | Display | ![]() |
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Full document | ![]() | 751.8 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ysbSC ![]() 6yuxC 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38484.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 292 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAP / |
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#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-PGR / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.03 M sodium chloride, 0.03 M sodium bromide, 0.03 M sodium iodide in 0.1 M MES/imidazole pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.5 Å / Num. obs: 67744 / % possible obs: 100 % / Redundancy: 12.47 % / CC1/2: 1 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 3301 / CC1/2: 0.517 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6YSB Resolution: 1.4→48.44 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.277 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 133.2 Å2 / Biso mean: 25.337 Å2 / Biso min: 13.7 Å2
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Refinement step | Cycle: final / Resolution: 1.4→48.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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