+Open data
-Basic information
Entry | Database: PDB / ID: 6xo3 | ||||||
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Title | ScoE with alpha-ketoglutarate in an off-site | ||||||
Components | ScoE protein | ||||||
Keywords | OXIDOREDUCTASE / isonitrile formation mononuclear iron dioxygenase | ||||||
Function / homology | Function and homology information (R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase / : / : / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coeruleorubidus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Jonnalagadda, R. / Drennan, C.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase. Authors: Jonnalagadda, R. / Del Rio Flores, A. / Cai, W. / Mehmood, R. / Narayanamoorthy, M. / Ren, C. / Zaragoza, J.P.T. / Kulik, H.J. / Zhang, W. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xo3.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xo3.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xo3_validation.pdf.gz | 761.2 KB | Display | wwPDB validaton report |
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Full document | 6xo3_full_validation.pdf.gz | 761.2 KB | Display | |
Data in XML | 6xo3_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 6xo3_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/6xo3 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/6xo3 | HTTPS FTP |
-Related structure data
Related structure data | 6xn6C 6xojC 6xpaC 6dchS C: citing same article (ref.) S: Starting model for refinement |
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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: 36882.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria) Gene: ScoE / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3B6UEU3 |
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#2: Chemical | ChemComp-AKG / |
#3: Chemical | ChemComp-FE2 / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 24% PEG 4000, 0.205 M Sodium Acetate, 0.1 M Tris pH 8.5, 1 mM alpha-ketoglutarate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 4, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→49.52 Å / Num. obs: 28221 / % possible obs: 99.9 % / Redundancy: 12.656 % / Biso Wilson estimate: 34.822 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.103 / Χ2: 0.827 / Net I/σ(I): 15.93 / Num. measured all: 357160 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DCH Resolution: 1.85→49.52 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.19 / Stereochemistry target values: ML
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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 max: 99.33 Å2 / Biso mean: 31.2632 Å2 / Biso min: 18.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→49.52 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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