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- PDB-7qaq: Crystal structure of a cyclodipeptide synthase from Parcubacteria... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qaq | ||||||
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Title | Crystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, E174A 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 | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 81.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.6 KB | Display | ![]() |
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Full document | ![]() | 426.3 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 | ![]() 7qatC ![]() 7qauC ![]() 7qawC ![]() 7qaxC ![]() 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: 27276.484 Da / Num. of mol.: 1 / Mutation: E174A 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: 2.33 Å3/Da / Density % sol: 47.2 % |
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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 PILATUS3 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: 2.4→51.3 Å / Num. obs: 10919 / % possible obs: 100 % / Redundancy: 23.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.032 / Rrim(I) all: 0.156 / Net I/σ(I): 26.1 / Num. measured all: 260322 / Scaling rejects: 4694 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QAE ![]() 7qae Resolution: 2.4→45.884 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.64 / 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: 137.49 Å2 / Biso mean: 55.3753 Å2 / Biso min: 23.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→45.884 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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