+Open data
-Basic information
Entry | Database: PDB / ID: 6siw | ||||||
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Title | PaaK family AMP-ligase with AMP | ||||||
Components | (PaaK-like ligase (AMP-dependent synthetase and ...) x 2 | ||||||
Keywords | LIGASE / PaaK like ligase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces sp. Tu 6176 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å | ||||||
Authors | Naismith, J.H. / Song, H. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility. Authors: Song, H. / Rao, C. / Deng, Z. / Yu, Y. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6siw.cif.gz | 366 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6siw.ent.gz | 294.3 KB | Display | PDB format |
PDBx/mmJSON format | 6siw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/6siw ftp://data.pdbj.org/pub/pdb/validation_reports/si/6siw | HTTPS FTP |
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-Related structure data
Related structure data | 6sixC 6siyC 6sizC 6sj0C 6sj1C 6sj2C 6sj3C 6sj4C 6tm4C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 5 - 435
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-Components
-PaaK-like ligase (AMP-dependent synthetase and ... , 2 types, 2 molecules AB
#1: Protein | Mass: 48289.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natL2, CF54_07380 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A022MRT4 |
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#2: Protein | Mass: 48360.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natL2, CF54_07380 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A022MRT4 |
-Non-polymers , 7 types, 278 molecules
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-7PE / | #9: 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: 2.52 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M KSCN, 0.1 M sodium citrate pH 6.0, 30% PEG MME 2K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0056 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0056 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→84.65 Å / Num. obs: 69487 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 10 % / Rmerge(I) obs: 0.901 / Num. unique obs: 3406 / CC1/2: 0.522 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.96→84.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.147 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.158 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.3 Å2 / Biso mean: 41.282 Å2 / Biso min: 18.54 Å2
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Refinement step | Cycle: final / Resolution: 1.96→84.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13236 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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