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- PDB-7qax: Crystal structure of a cyclodipeptide synthase from Parcubacteria... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qax | ||||||
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Title | Crystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, E171Q mutant | ||||||
![]() | Cyclodipeptide synthase | ||||||
![]() | LIGASE / Cyclodipeptide synthase | ||||||
Function / homology | Cyclodipeptide synthase superfamily / Cyclodipeptide synthase / Cyclodipeptide synthase / aminoacyltransferase activity / Cyclodipeptide synthase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sutherland, E. / Harding, C.J. / Czekster, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Active site remodelling of a cyclodipeptide synthase redefines substrate scope. Authors: Sutherland, E. / Harding, C.J. / Czekster, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.4 KB | Display | ![]() |
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PDB format | ![]() | 83.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.2 KB | Display | ![]() |
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Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qaqC ![]() 7qatC ![]() 7qauC ![]() 7qawC ![]() 7qayC ![]() 7qb8C ![]() 7qae S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 27333.535 Da / Num. of mol.: 1 / Mutation: E171Q Source method: isolated from a genetically manipulated source Details: C-terminal His Tag (EHHHHHH) Source: (gene. exp.) ![]() Gene: O210_OD1C00001G0241 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.27 M Ammonium sulfate 0.1 M sodium acetate pH 5.17 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.089→46.051 Å / Num. obs: 222211 / % possible obs: 92.57 % / Redundancy: 14.5 % / CC1/2: 0.999 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.09→2.16 Å / Rmerge(I) obs: 1.637 / Num. unique obs: 1565 / CC1/2: 0.331 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QAE ![]() 7qae Resolution: 2.089→46.051 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.12 Å2 / Biso mean: 68.1625 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.089→46.051 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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