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- PDB-5fr7: Erwinia amylovora AmyR amylovoran repressor, a member of the YbjN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fr7 | ||||||
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Title | Erwinia amylovora AmyR amylovoran repressor, a member of the YbjN protein family | ||||||
![]() | AMYR | ||||||
![]() | SIGNALING PROTEIN / 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 | ![]() | 69.3 KB | Display | ![]() |
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PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5frkSC S: Starting model for refinement C: citing same article ( |
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Similar 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: 18042.807 Da / Num. of mol.: 2 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: 3.08 Å3/Da / Density % sol: 60.12 % / Description: NONE |
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Crystal grow | pH: 6.9 Details: 0.1M SODIUM CACODYLATE PH 6.9, 0.2M MAGNESIUM CHLORIDE, 46% (V/V) PEG200 |
-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: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→53.26 Å / Num. obs: 29587 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.95→2.14 Å / Redundancy: 5 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SPDB ENTRY 5FRK Resolution: 1.95→53.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.423 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY OLIGOMERIC STATE IS UNCERTAIN
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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: 42.392 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→53.26 Å
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Refine LS restraints |
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