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- PDB-7x2x: Crystal Structure of hetero-Diels-Alderase PycR1 in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x2x | ||||||
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Title | Crystal Structure of hetero-Diels-Alderase PycR1 in complex with 10-hydroxy-8E-humulene | ||||||
![]() | PycR1 | ||||||
![]() | BIOSYNTHETIC PROTEIN / Complex | ||||||
Function / homology | Chem-80N![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J. / Lu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Calcium-dependent glycosylated enzyme in the tandem hetero-Diels-Alder reaction 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 | ![]() | 123.6 KB | Display | ![]() |
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PDB format | ![]() | 74.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7x2sC ![]() 7x36C ![]() 7x2nS S: Starting model for refinement C: citing same article ( |
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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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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: 42954.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(6-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-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 Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 474 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/80N.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/80N.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / | ||||
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#5: Chemical | ChemComp-80N / ( | ||||
#6: Chemical | ChemComp-CA / | ||||
#7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-CL / #9: 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: 2.93 Å3/Da / Density % sol: 58.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH=6.0, 0.2 M Ammonium chloride, 20%(w/v) PEG6000 |
-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: Oct 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: 1.58→45.93 Å / Num. obs: 70881 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 25.5 % / Rmerge(I) obs: 1.699 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3458 / CC1/2: 0.804 / Rpim(I) all: 0.484 / Rrim(I) all: 1.767 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7X2N Resolution: 1.58→45.93 Å / SU ML: 0.1524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5657 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: 29.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→45.93 Å
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Refine LS restraints |
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LS refinement shell |
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