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Open data
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Basic information
Entry | Database: PDB / ID: 8ra0 | |||||||||||||||
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Title | Crystal structure of CysF | |||||||||||||||
![]() | AMP-dependent synthetase | |||||||||||||||
![]() | BIOSYNTHETIC PROTEIN / Beta lactone formation | |||||||||||||||
Function / homology | ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / CITRATE ANION / AMP-dependent synthetase![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Levy, C.W. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryptic enzymatic assembly of peptides armed with beta-lactone warheads. Authors: Xu, G. / Torri, D. / Cuesta-Hoyos, S. / Panda, D. / Yates, L.R.L. / Zallot, R. / Bian, K. / Jia, D. / Iorgu, A.I. / Levy, C. / Shepherd, S.A. / Micklefield, J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.2 KB | Display | ![]() |
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PDB format | ![]() | 232 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 459.1 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 54399.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PG4 / |
#3: Chemical | ChemComp-FLC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: JCSG Plus A2 0.1 M Sodium citrate 5.5 20 % w/v PEG 3000 Temp details: Cold Room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50.65 Å / Num. obs: 35828 / % possible obs: 99.56 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.08 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.0991 / Net I/σ(I): 5.97 |
Reflection shell | Resolution: 1.89→1.958 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 3488 / CC1/2: 0.419 / Rpim(I) all: 0.83 / % possible all: 97.34 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→50.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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