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Open data
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Basic information
Entry | Database: PDB / ID: 7x2n | ||||||
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Title | Crystal structure of Diels-Alderase PycR1 | ||||||
![]() | PycR1 | ||||||
![]() | BIOSYNTHETIC PROTEIN / Diels-Alderase | ||||||
Function / homology | alpha-D-mannopyranose![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J. / Lu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of hetero-Diels-Alderase PycR1 Authors: Zhou, J. / Lu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.8 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p4oS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42954.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/MAN.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: Sugar | ChemComp-MAN / |
-Non-polymers , 4 types, 481 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / | ||||
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#6: Chemical | #7: Chemical | ChemComp-CA / | #8: 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: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-Sodium citrate, 20% (w/v)PEG4000, 5% (w/v)Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 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: 1.72→45.89 Å / Num. obs: 55134 / % possible obs: 100 % / Redundancy: 25.7 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.023 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.72→1.75 Å / Rmerge(I) obs: 1.778 / Num. unique obs: 2891 / CC1/2: 0.806 / Rpim(I) all: 0.503 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2p4o Resolution: 1.72→44.83 Å / SU ML: 0.179 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8603 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: 33.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→44.83 Å
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Refine LS restraints |
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LS refinement shell |
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