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Open data
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Basic information
Entry | Database: PDB / ID: 5sy4 | ||||||
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Title | Atomic resolution structure of reduced E. coli YajL | ||||||
![]() | Chaperone YajL | ||||||
![]() | CHAPERONE / DJ-1/PfpI superfamily nucleophile elbow | ||||||
Function / homology | ![]() protein repair / glyoxal metabolic process / glycolate biosynthetic process / protein deglycase / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / ribosome biogenesis / cellular response to oxidative stress ...protein repair / glyoxal metabolic process / glycolate biosynthetic process / protein deglycase / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / Hydrolases; Acting on ester bonds; Thioester hydrolases / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / ribosome biogenesis / cellular response to oxidative stress / response to heat / protein refolding / hydrolase activity / DNA repair / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilson, M.A. / Lin, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Authors: Lin, J. / Pozharski, E. / Wilson, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.1 KB | Display | ![]() |
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PDB format | ![]() | 162 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.8 KB | Display | ![]() |
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Full document | ![]() | 429 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5sy6C ![]() 5sy9C ![]() 5syaC ![]() 2ab0S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 196 / Label seq-ID: 5 - 199
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Components
#1: Protein | Mass: 21080.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: thiJ, ACU57_11870, AM266_04520, ERS085365_02411, ERS085416_01937, ERS139211_01908, ERS150873_01827, PU15_11320, PU38_04800, SK85_00449 Plasmid: pET15b / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: polyethylene glycol 4000, Tris HCl, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2015 Details: Rh coated collimating mirrors, K-B focusing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.73 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→38 Å / Num. obs: 191363 / % possible obs: 97.6 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 0.98→1 Å / Redundancy: 9.5 % / Rmerge(I) obs: 2.393 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.479 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AB0 Resolution: 0.98→61.52 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.663 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.354 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→61.52 Å
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Refine LS restraints |
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