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- PDB-7y3h: Crystal Structure of Diels-Alderase ApiI in complex with SAM and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y3h | ||||||
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Title | Crystal Structure of Diels-Alderase ApiI in complex with SAM and product | ||||||
![]() | ApiI | ||||||
![]() | BIOSYNTHETIC PROTEIN / Complex | ||||||
Function / homology | Chem-IAH / S-ADENOSYLMETHIONINE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J.H. / Lu, J.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Diels-Alderase ApiI in complex with SAM and product Authors: Zhou, J.H. / Lu, J.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 981.8 KB | Display | ![]() |
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Full document | ![]() | 989.3 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wupS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44364.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 205 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IAH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IAH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAM / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-IAH / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M Na nitrate, 0.1M Bis Tris propane pH 7.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→49.23 Å / Num. obs: 32310 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 34.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2247 / CC1/2: 0.908 / Rpim(I) all: 0.371 / Rrim(I) all: 0.993 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WUP Resolution: 1.97→42.64 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9776 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→42.64 Å
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Refine LS restraints |
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LS refinement shell |
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