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Yorodumi- PDB-8tww: Crystal structure of nitrile synthase AetD with substrate bound a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tww | |||||||||||||||
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Title | Crystal structure of nitrile synthase AetD with substrate bound and cofactor fully assembled | |||||||||||||||
Components | AetD | |||||||||||||||
Keywords | OXIDOREDUCTASE / nitrile synthase / non-heme iron enzyme / diiron enzyme | |||||||||||||||
Function / homology | Haem oxygenase-like, multi-helical / metal ion binding / Chem-67I / : / AetD Function and homology information | |||||||||||||||
Biological species | Aetokthonos hydrillicola (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | |||||||||||||||
Authors | Ye, N. / Drennan, C.L. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat.Chem. / Year: 2024 Title: A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile. Authors: Adak, S. / Ye, N. / Calderone, L.A. / Duan, M. / Lubeck, W. / Schafer, R.J.B. / Lukowski, A.L. / Houk, K.N. / Pandelia, M.E. / Drennan, C.L. / Moore, B.S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tww.cif.gz | 235.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tww.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 8tww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tww_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8tww_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8tww_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 8tww_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/8tww ftp://data.pdbj.org/pub/pdb/validation_reports/tw/8tww | HTTPS FTP |
-Related structure data
Related structure data | |
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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: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.999949086615, -0.00477341593085, -0.00889036992855), (0.00985781204618, -0.273870873823, -0.961715949755), (0.00215585685457, -0.961754625137, 0.273903985567)Vector: ...NCS oper: (Code: given Matrix: (-0.999949086615, -0.00477341593085, -0.00889036992855), Vector: |
-Components
#1: Protein | Mass: 30640.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aetokthonos hydrillicola (bacteria) / Gene: aetD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A861B387 #2: Chemical | #3: Chemical | ChemComp-FE / #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: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 250 mM ammonium sulfate, 20% w/v PEG 3350 |
-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: 0.9792 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 23, 2022 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 40402 / % possible obs: 98.7 % / Redundancy: 9 % / Biso Wilson estimate: 30.17 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 2→2.13 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 6430 / CC1/2: 0.937 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→46.98 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5788 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.070062546 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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