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Yorodumi- PDB-5g17: Bordetella Alcaligenes HDAH (T101A) bound to 9,9,9-trifluoro-8,8-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g17 | ||||||
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Title | Bordetella Alcaligenes HDAH (T101A) bound to 9,9,9-trifluoro-8,8- dihydroxy-N-phenylnonanamide. | ||||||
Components | HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE | ||||||
Keywords | HYDROLASE / HDAH / HDAC / HDLP | ||||||
Function / homology | Function and homology information 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 | ALCALIGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Kraemer, A. / Meyer-Almes, F.J. / Yildiz, O. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Authors: Meyners, C. / Kramer, A. / Yildiz, O. / Meyer-Almes, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g17.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g17.ent.gz | 261.9 KB | Display | PDB format |
PDBx/mmJSON format | 5g17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g17_validation.pdf.gz | 933.6 KB | Display | wwPDB validaton report |
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Full document | 5g17_full_validation.pdf.gz | 947.6 KB | Display | |
Data in XML | 5g17_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 5g17_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g17 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g17 | HTTPS FTP |
-Related structure data
Related structure data | 5g1aC 5g1bC 1zz0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39401.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ALCALIGENES (bacteria) / Strain: FB188 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: Q70I53, amidase #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03895 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03895 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→25 Å / Num. obs: 142442 / % possible obs: 100 % / Observed criterion σ(I): 2.7 / Redundancy: 11.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.51→1.54 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZZ0 Resolution: 1.51→87.68 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.113 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.053 / 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: 16.226 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→87.68 Å
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Refine LS restraints |
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