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- PDB-5g3w: Structure of HDAC like protein from Bordetella Alcaligenes in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g3w | |||||||||
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Title | Structure of HDAC like protein from Bordetella Alcaligenes in complex with the photoswitchable inhibitor CEW65 | |||||||||
![]() | HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE | |||||||||
![]() | HYDROLASE / HDAH / HDAC / HDLP | |||||||||
Function / homology | ![]() Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase 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. | |||||||||
![]() | ![]() 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 | ![]() | 633.8 KB | Display | ![]() |
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PDB format | ![]() | 524.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 74.2 KB | Display | |
Data in CIF | ![]() | 109.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g1cC ![]() 5li3C ![]() 1zz0S ![]() 5g3v 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40122.281 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1820 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/C65.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/C65.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-C65 / ( #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.3 % / Description: NONE |
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Crystal grow | pH: 5.25 / Details: PEG 400 MALATE IMIDAZOLE PH 5.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20.67 Å / Num. obs: 197317 / % possible obs: 99.7 % / Observed criterion σ(I): 2.9 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZZ0 Resolution: 1.6→125.57 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.126 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→125.57 Å
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Refine LS restraints |
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