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- PDB-8pyx: Amide bond synthetase from Streptomyces hindustanus K492H mutant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pyx | ||||||
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Title | Amide bond synthetase from Streptomyces hindustanus K492H mutant in complex with Adenosine | ||||||
![]() | Fatty-acyl-CoA synthase | ||||||
![]() | LIGASE / Amide / Amide Bond Synthetase / ATP | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, Q. / Grogan, G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.7 KB | Display | ![]() |
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PDB format | ![]() | 162.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 59.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pppC ![]() 8pyyC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() Gene: SAMN05444320_10350 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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Refine LS restraints |
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