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Yorodumi- PDB-8aut: WelO5* L221A bound to Zn(II), Cl, 2-oxoglutarate, and 12-epi-hapa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aut | ||||||
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Title | WelO5* L221A bound to Zn(II), Cl, 2-oxoglutarate, and 12-epi-hapalindole C | ||||||
Components | Oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / WelO5* 2-oxoglutarate-dependent halogenase / 12-epi-hapalindole C | ||||||
Function / homology | 2-OXOGLUTARIC ACID / Chem-OAU / Oxidoreductase Function and homology information | ||||||
Biological species | Hapalosiphon welwitschii UH IC-52-3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.685 Å | ||||||
Authors | Buller, R. / Hueppi, S. / Voss, M. / Schaub, D. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Chemcatchem / Year: 2022 Title: Enzyme engineering enables inversion of substrate stereopreference of the halogenase WelO5* Authors: Voss, M. / Huppi, S. / Schaub, D. / Hayashi, T. / Ligibel, M. / Sager, E. / Schroer, K. / Snajdrova, R. / Buller, R.M.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aut.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8aut.ent.gz | 725.5 KB | Display | PDB format |
PDBx/mmJSON format | 8aut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aut_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8aut_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8aut_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 8aut_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/8aut ftp://data.pdbj.org/pub/pdb/validation_reports/au/8aut | HTTPS FTP |
-Related structure data
Related structure data | 8acvSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 11 - 290 / Label seq-ID: 31 - 310
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34569.875 Da / Num. of mol.: 4 / Mutation: L221A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hapalosiphon welwitschii UH IC-52-3 (bacteria) Gene: welO15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075X7C6 |
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-Non-polymers , 7 types, 130 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-AKG / #5: Chemical | ChemComp-OAU / #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-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: 2.41 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG-4000, 200 mM LiSO4, in 100 mM TRIS pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000009 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→49.17 Å / Num. obs: 37222 / % possible obs: 99.9 % / Redundancy: 38.9 % / Biso Wilson estimate: 67.52 Å2 / CC1/2: 1 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.68→2.8 Å / Num. unique obs: 4433 / CC1/2: 0.782 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8ACV Resolution: 2.685→49.17 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 34.206 / SU ML: 0.305 / Cross valid method: FREE R-VALUE / ESU R Free: 0.319 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.612 Å2
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Refinement step | Cycle: LAST / Resolution: 2.685→49.17 Å
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Refine LS restraints |
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