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Yorodumi- PDB-6ytz: Crystal structure of Malus domestica Double Bond Reductase (MdDBR... -
+Open data
-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 | ||||||
Components | Double Bond Reductase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / phenylpropanoid pathway / double bond reductase / Malus domestica | ||||||
Function / homology | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / R-1,2-PROPANEDIOL Function and homology information | ||||||
Biological species | Malus domestica (apple) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Caliandro, R. / Polsinelli, I. / Demitri, N. / Benini, S. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ytz.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ytz.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ytz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ytz_validation.pdf.gz | 748.4 KB | Display | wwPDB validaton report |
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Full document | 6ytz_full_validation.pdf.gz | 751.8 KB | Display | |
Data in XML | 6ytz_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6ytz_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6ytz ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6ytz | HTTPS FTP |
-Related structure data
Related structure data | 6ysbSC 6yuxC 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 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.) Malus domestica (apple) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 6 types, 292 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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