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Yorodumi- PDB-5iqu: WelO5 G166D variant bound to Fe(II), 2-oxoglutarate, and 12-epifi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iqu | ||||||
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Title | WelO5 G166D variant bound to Fe(II), 2-oxoglutarate, and 12-epifischerindole U | ||||||
Components | WelO5 | ||||||
Keywords | OXIDOREDUCTASE / metalloenzyme halogenase 2-oxoglutarate | ||||||
Function / homology | metal ion binding / Chem-6CU / 2-OXOGLUTARIC ACID / : / WelO5 Function and homology information | ||||||
Biological species | Hapalosiphon welwitschii UTEX B 1830 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Mitchell, A.J. / Maggiolo, A.O. / Boal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5. Authors: Mitchell, A.J. / Zhu, Q. / Maggiolo, A.O. / Ananth, N.R. / Hillwig, M.L. / Liu, X. / Boal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iqu.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iqu.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 5iqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iqu_validation.pdf.gz | 781.3 KB | Display | wwPDB validaton report |
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Full document | 5iqu_full_validation.pdf.gz | 781.8 KB | Display | |
Data in XML | 5iqu_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5iqu_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqu ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqu | HTTPS FTP |
-Related structure data
Related structure data | 5iqsSC 5iqtC 5iqvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35587.980 Da / Num. of mol.: 1 / Mutation: G166D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hapalosiphon welwitschii UTEX B 1830 (bacteria) Strain: UTEX B 1830 / Plasmid: pQTEV / Details (production host): N-term. 6xhis-tag; ampicillin / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: A0A067YX61 |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-6CU / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.51 % / Description: Long needles/rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.1 M Bis-tris pH 5.5, 0.1 M sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.03 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 8378 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Net I/av σ(I): 21.182 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IQS Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.135 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.01 Å2 / Biso mean: 50.748 Å2 / Biso min: 27.88 Å2
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Refinement step | Cycle: final / Resolution: 2.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.573 Å / Total num. of bins used: 20
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