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Yorodumi- PDB-7x2x: Crystal Structure of hetero-Diels-Alderase PycR1 in complex with ... -
+Open data
-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 | ||||||
Components | PycR1 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Complex | ||||||
Function / homology | Chem-80N Function and homology information | ||||||
Biological species | Leptobacillium sp. (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Zhou, J. / Lu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x2x.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x2x.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 7x2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/7x2x ftp://data.pdbj.org/pub/pdb/validation_reports/x2/7x2x | HTTPS FTP |
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-Related structure data
Related structure data | 7x2sC 7x36C 7x2nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Leptobacillium sp. (fungus) / Production host: Escherichia coli (E. coli) |
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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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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