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Yorodumi- PDB-8pyy: Amide bond synthetase from Streptomyces hindustanus in open confo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pyy | ||||||
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Title | Amide bond synthetase from Streptomyces hindustanus in open conformation | ||||||
Components | Fatty-acyl-CoA synthase | ||||||
Keywords | LIGASE / Amide / Amide Bond Synthetase / ATP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tang, Q. / Grogan, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2024 Title: Broad Spectrum Enantioselective Amide Bond Synthetase from Streptoalloteichus hindustanus. Authors: Tang, Q. / Petchey, M. / Rowlinson, B. / Burden, T.J. / Fairlamb, I.J.S. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pyy.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pyy.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/8pyy ftp://data.pdbj.org/pub/pdb/validation_reports/py/8pyy | HTTPS FTP |
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-Related structure data
Related structure data | 8pppC 8pyxC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54441.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces (bacteria) / Gene: SAMN05444320_10350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M5ABR5 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.62 Å3/Da / Density % sol: 78.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.8 M Li2SO4; 0.1M bis-tris propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95374 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→57.32 Å / Num. obs: 28308 / % possible obs: 100 % / Redundancy: 40.1 % / Biso Wilson estimate: 48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.34 / Rpim(I) all: 0.05 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.9→3.08 Å / Rmerge(I) obs: 1.93 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4468 / CC1/2: 0.83 / Rpim(I) all: 0.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→57.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.577 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.576 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→57.32 Å
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Refine LS restraints |
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