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Yorodumi- PDB-8hsn: Crystal structure of DFA I-forming Inulin Lyase from Streptomyces... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hsn | ||||||
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Title | Crystal structure of DFA I-forming Inulin Lyase from Streptomyces peucetius subsp. caesius ATCC 27952 | ||||||
Components | Fructotransferase | ||||||
Keywords | LYASE / right-handed beta-helix protein / DFA I-forming inulin lyase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces peucetius subsp. caesius ATCC 27952 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Cheng, M. / Rao, Y.J. / Mu, W.M. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of DFA I-forming Inulin Lyase from Streptomyces peucetius subsp. caesius ATCC 27952 Authors: Mu, W.M. / Rao, Y.J. / Cheng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hsn.cif.gz | 436.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hsn.ent.gz | 362.3 KB | Display | PDB format |
PDBx/mmJSON format | 8hsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/8hsn ftp://data.pdbj.org/pub/pdb/validation_reports/hs/8hsn | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42752.516 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces peucetius subsp. caesius ATCC 27952 (bacteria) Gene: CGZ69_03210 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A2D3U3Z1, inulin fructotransferase (DFA-I-forming) |
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-Non-polymers , 6 types, 603 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.59 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES monohydrate, 12% Polyethylene glycol 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→47.81 Å / Num. obs: 147518 / % possible obs: 99 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.69→1.75 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 14488 / CC1/2: 0.969 / Rrim(I) all: 0.374 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→47.81 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→47.81 Å
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Refine LS restraints |
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LS refinement shell |
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