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Yorodumi- PDB-8pyx: Amide bond synthetase from Streptomyces hindustanus K492H mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pyx | ||||||
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Title | Amide bond synthetase from Streptomyces hindustanus K492H mutant in complex with Adenosine | ||||||
Components | Fatty-acyl-CoA synthase | ||||||
Keywords | LIGASE / Amide / Amide Bond Synthetase / ATP | ||||||
Function / homology | Function and homology information ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme Similarity search - Domain/homology | ||||||
Biological species | Streptoalloteichus hindustanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 | 8pyx.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pyx.ent.gz | 162.5 KB | Display | PDB format |
PDBx/mmJSON format | 8pyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/8pyx ftp://data.pdbj.org/pub/pdb/validation_reports/py/8pyx | HTTPS FTP |
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-Related structure data
Related structure data | 8pppC 8pyyC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54450.410 Da / Num. of mol.: 2 / Mutation: K492H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria) Gene: SAMN05444320_10350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M5ABR5 #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Li2SO4; 0.1 M HEPES pH 7.5; 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95881 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95881 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→29.35 Å / Num. obs: 78528 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.06 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.02→2.06 Å / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3766 / CC1/2: 0.8 / Rpim(I) all: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→29.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.316 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.177 / 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: 30.238 Å2
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Refinement step | Cycle: 1 / Resolution: 2.02→29.35 Å
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