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Open data
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Basic information
Entry | Database: PDB / ID: 7x36 | ||||||
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Title | Crystal Structure of hetero-Diels-Alderase EupfF | ||||||
![]() | EupfF | ||||||
![]() | BIOSYNTHETIC PROTEIN / hetero-Diels-Alderase | ||||||
Function / homology | BENZOIC ACID / alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER![]() | ||||||
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 | ![]() | 390.7 KB | Display | ![]() |
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PDB format | ![]() | 255.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 62.1 KB | Display | |
Data in CIF | ![]() | 91.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x2sC ![]() 7x2xC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41382.387 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 5 types, 18 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #5: Sugar | ChemComp-NAG / #11: Sugar | ChemComp-MAN / | |
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-Non-polymers , 6 types, 1170 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-CA / #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Chemical | ChemComp-GOL / | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate, PH=5.0, 20%(w/v) PEG4000 |
-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: Sep 21, 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: 1.92→46.9 Å / Num. obs: 146341 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.059 / Rrim(I) all: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2 / Num. unique obs: 7184 / CC1/2: 0.848 / Rpim(I) all: 0.515 / Rrim(I) all: 0.871 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7X2N Resolution: 1.92→46.9 Å / SU ML: 0.2514 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3735 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: 31.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→46.9 Å
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Refine LS restraints |
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LS refinement shell |
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