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- PDB-7dvi: Crystal Structure of AbnU: An exo-specific intermolecular Diels-A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dvi | ||||||||||||
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Title | Crystal Structure of AbnU: An exo-specific intermolecular Diels-Alderase | ||||||||||||
![]() | AOC_like domain-containing protein | ||||||||||||
![]() | ISOMERASE / Diels ALderase | ||||||||||||
Function / homology | Allene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / AOC_like domain-containing protein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Kashyap, R. / Addlagatta, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Exo-selective intermolecular Diels-Alder reaction by PyrI4 and AbnU on non-natural substrates. Authors: Kashyap, R. / Yerra, N.V. / Oja, J. / Bala, S. / Potuganti, R. / Thota, J.R. / Alla, M. / Pal, D. / Addlagatta, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.7 KB | Display | ![]() |
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PDB format | ![]() | 31.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dvkC ![]() 5dyvS 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
#1: Protein | Mass: 17071.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M Imidazole, pH 7.0, 20% Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 28, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.974 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→45.26 Å / Num. obs: 15158 / % possible obs: 99.9 % / Redundancy: 36.4 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.011 / Rrim(I) all: 0.065 / Net I/σ(I): 40.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5DYV Resolution: 2→45.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.591 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.147 / 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: 91.81 Å2 / Biso mean: 36.25 Å2 / Biso min: 22.22 Å2
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Refinement step | Cycle: final / Resolution: 2→45.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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