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Yorodumi- PDB-7szg: Structure of the Rieske Non-heme Iron Oxygenase GxtA Pressurized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7szg | ||||||
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Title | Structure of the Rieske Non-heme Iron Oxygenase GxtA Pressurized with Xenon | ||||||
Components | SxtDIOX | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Saxitoxin GxtA Rieske oxygenase metalloprotein iron-sulfur cluster non-heme iron | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Microseira wollei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Bridwell-Rabb, J. / Liu, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Design principles for site-selective hydroxylation by a Rieske oxygenase. Authors: Liu, J. / Tian, J. / Perry, C. / Lukowski, A.L. / Doukov, T.I. / Narayan, A.R.H. / Bridwell-Rabb, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7szg.cif.gz | 229.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7szg.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 7szg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/7szg ftp://data.pdbj.org/pub/pdb/validation_reports/sz/7szg | HTTPS FTP |
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-Related structure data
Related structure data | 7szeC 7szfC 7szhC 6wncS 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 38243.387 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microseira wollei (bacteria) / Gene: sxtDIOX / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: C3RVP5 |
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-Non-polymers , 7 types, 276 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #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: 2.44 Å3/Da / Density % sol: 49.59 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.3 M MgCl2, 0.1 M Bis-Tris pH 5.5, 25% v/v PEG3350, 15% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 2.06633 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.06633 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. obs: 59952 / % possible obs: 99.7 % / Redundancy: 18.5 % / Biso Wilson estimate: 55.26 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.141 / Net I/σ(I): 19.63 |
Reflection shell | Resolution: 2.69→2.76 Å / Redundancy: 17.45 % / Mean I/σ(I) obs: 2.42 / Num. unique obs: 4447 / CC1/2: 0.793 / Rrim(I) all: 1.393 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WNC Resolution: 2.69→48.47 Å / SU ML: 0.4168 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0309 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 50.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→48.47 Å
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Refine LS restraints |
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LS refinement shell |
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