+Open data
-Basic information
Entry | Database: PDB / ID: 8szt | ||||||
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Title | Structure of Kdac1 from Acinetobacter baumannii | ||||||
Components | Histone deacetylase domain-containing protein | ||||||
Keywords | HYDROLASE / histone deacetylase / metallohydrolase | ||||||
Function / homology | Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / : / Histone deacetylase domain-containing protein Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Watson, P.R. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Structure and Function of Kdac1, a Class II Deacetylase from the Multidrug-Resistant Pathogen Acinetobacter baumannii . Authors: Watson, P.R. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8szt.cif.gz | 340.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8szt.ent.gz | 219.3 KB | Display | PDB format |
PDBx/mmJSON format | 8szt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/8szt ftp://data.pdbj.org/pub/pdb/validation_reports/sz/8szt | HTTPS FTP |
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-Related structure data
Related structure data | 8szuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40439.953 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R8YPJ7 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: Kdac1 10mg/mL 0.6 M sodium formate and 20% (w/v) polyethylene glycol 3,350 Seeded |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→96.53 Å / Num. obs: 55541 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.969 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.5→2.57 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 36436 / CC1/2: 0.548 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→60.51 Å / SU ML: 0.3582 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.413 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→60.51 Å
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Refine LS restraints |
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LS refinement shell |
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