+Open data
-Basic information
Entry | Database: PDB / ID: 6zyl | ||||||
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Title | non-heme monooxygenase; ThoJ apo | ||||||
Components | Uncharacterized protein | ||||||
Keywords | METAL BINDING PROTEIN / non-heme deoxygenate / ThoJ | ||||||
Function / homology | Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / L(+)-TARTARIC ACID / Phytanoyl-CoA dioxygenase Function and homology information | ||||||
Biological species | Streptomyces malaysiense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Koehnke, J. / Sikandar, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Non-Heme Monooxygenase ThoJ Catalyzes Thioholgamide beta-Hydroxylation. Authors: Sikandar, A. / Lopatniuk, M. / Luzhetskyy, A. / Koehnke, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zyl.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zyl.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zyl ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zyl | HTTPS FTP |
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-Related structure data
Related structure data | 6zykC 5ncjS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33578.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces malaysiense (bacteria) / Gene: VT52_024865 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1J4PXK4 |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 150 mM Sodium tartrate, 28% (w/v) PEG 3350, 10% (v/v) 2.0 M NDSB-221 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→42.85 Å / Num. obs: 26006 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.996 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.09→2.15 Å / Num. unique obs: 1981 / CC1/2: 0.788 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NCJ Resolution: 2.09→42.85 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.83 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→42.85 Å
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Refine LS restraints |
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LS refinement shell |
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