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- PDB-5frk: SeMet crystal structure of Erwinia amylovora AmyR amylovoran repr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5frk | ||||||
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Title | SeMet crystal structure of Erwinia amylovora AmyR amylovoran repressor, a member of the YbjN protein family | ||||||
![]() | AMYR | ||||||
![]() | TRANSCRIPTION / AMYLOVORAN / YBJN / FIRE BLIGHT / PLANT PATHOGEN / T3SS | ||||||
Function / homology | Putative sensory transduction regulator YbjN / Putative bacterial sensory transduction regulator / Uncharacterized protein ybjN![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bartho, J.D. / Bellini, D. / Wuerges, J. / Demitri, N. / Walsh, M. / Benini, S. | ||||||
![]() | ![]() Title: The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions. Authors: Bartho, J.D. / Bellini, D. / Wuerges, J. / Demitri, N. / Toccafondi, M. / Schmitt, A.O. / Zhao, Y. / Walsh, M.A. / Benini, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.7 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 18464.859 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | N-TERMINAL GA ADDED FROM TEV PROTEASE CLEAVAGE SITE. H2G MUTATION A CLONING ARTEFACT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.66 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 7.3 Details: 0.1 M SODIUM CACODYLATE PH7.3 0.3 M MAGNESIUM CHLORIDE, 42% PEG 200, 293 K PROTEIN CONCENTRATION 8 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→53.34 Å / Num. obs: 22681 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / % possible all: 75.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.12→69.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.146 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. INSUFFICIENT EVIDENCE TO CONFIRM TETRAMERIC STATE IN SOLUTION.
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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: 49.904 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→69.01 Å
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Refine LS restraints |
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