+Open data
-Basic information
Entry | Database: PDB / ID: 7x36 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of hetero-Diels-Alderase EupfF | ||||||
Components | EupfF | ||||||
Keywords | BIOSYNTHETIC PROTEIN / hetero-Diels-Alderase | ||||||
Function / homology | BENZOIC ACID / alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Penicillium janthinellum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Zhou, J. / Lu, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Calcium-dependent glycosylated enzyme in the tandem hetero-Diels-Alder reaction Authors: Zhou, J. / Lu, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7x36.cif.gz | 390.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7x36.ent.gz | 255.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/7x36 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/7x36 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7x2sC 7x2xC 7x2nS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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.) Penicillium janthinellum (fungus) / Production host: Escherichia coli (E. coli) |
---|
-Sugars , 5 types, 18 molecules
#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 / | |
---|
-Non-polymers , 6 types, 1170 molecules
#6: Chemical | ChemComp-CA / #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Chemical | ChemComp-GOL / | #12: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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. |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|