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- PDB-5li3: Crystal structure of HDAC-like protein from P. aeruginosa in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5li3 | ||||||
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Title | Crystal structure of HDAC-like protein from P. aeruginosa in complex with a photo-switchable inhibitor. | ||||||
![]() | Acetoin utilization protein | ||||||
![]() | SIGNALING PROTEIN / Histone deacetylase / Histone Deacetylase Inhibitors / HDAH | ||||||
Function / homology | ![]() Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / hydrolase activity / negative regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kraemer, A. / Meyer-Almes, F.J. / Yildiz, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. Authors: Weston, C.E. / Kramer, A. / Colin, F. / Yildiz, O. / Baud, M.G. / Meyer-Almes, F.J. / Fuchter, M.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 | ![]() | 157.6 KB | Display | ![]() |
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PDB format | ![]() | 122.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763.3 KB | Display | ![]() |
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Full document | ![]() | 769.5 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g1cC ![]() 5g3wC ![]() 5g0xS 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: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 369 / Label seq-ID: 3 - 369
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Components
#1: Protein | Mass: 41098.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.5M potassium hydrogen phosphate 0.5M sodium hydrogen phosphate 0.1M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0002 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→32 Å / Num. obs: 41043 / % possible obs: 100 % / Observed criterion σ(F): 2.5 / Redundancy: 11.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.84 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5g0x Resolution: 2.4→32 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.055 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.298 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.624 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→32 Å
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Refine LS restraints |
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