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Yorodumi- PDB-7txy: Crystal structure of the 2-Aminophenol 1,6-dioxygenase from the A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7txy | ||||||
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Title | Crystal structure of the 2-Aminophenol 1,6-dioxygenase from the ARO bacterial microcompartment of Micromonospora rosaria | ||||||
Components |
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Keywords | OXIDOREDUCTASE / 2-aminophenol / dioxygenase | ||||||
Function / homology | Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / : / dioxygenase activity / ferrous iron binding / : / 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha Function and homology information | ||||||
Biological species | Micromonospora rosaria (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Sutter, M. / Doron, L. / Kerfeld, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mbio / Year: 2023 Title: Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria. Authors: Doron, L. / Sutter, M. / Kerfeld, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7txy.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7txy.ent.gz | 700.9 KB | Display | PDB format |
PDBx/mmJSON format | 7txy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7txy ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txy | HTTPS FTP |
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-Related structure data
Related structure data | 3vsgS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 30395.928 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora rosaria (bacteria) / Gene: AWW66_10320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A136PV43 #2: Protein | Mass: 37399.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora rosaria (bacteria) / Gene: AWW66_10325 / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-FE2 / #4: Water | ChemComp-HOH / | 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 28% PEG 8000, 400mM Ammonium acetate, 0.1M Tris pH 8.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.5 Å / Num. obs: 230720 / % possible obs: 97.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.173 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11288 / CC1/2: 0.421 / Rrim(I) all: 1.659 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VSG Resolution: 1.75→46.14 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.5452 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: 40.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.14 Å
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Refine LS restraints |
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LS refinement shell |
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