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Yorodumi- PDB-9gkx: Crystal Structure of Rhizorhabdus wittichii Dimethoate hydrolase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9gkx | |||||||||
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Title | Crystal Structure of Rhizorhabdus wittichii Dimethoate hydrolase (DmhA) in complex with SAHA | |||||||||
Components | Dimethoate hydrolase | |||||||||
Keywords | HYDROLASE / Inhibitor / SAHA / Deacetylase / Deacylase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Rhizorhabdus wittichii DC-6 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Graf, L.G. / Lammers, M. / Schulze, S. / Palm, G.J. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nature Communications / Year: 2024 Title: Distribution and diversity of classical deacylases in bacteria Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoeker, O. / Wang, N. / Hocking, D. / Jebeli, L. / Girbardt, B. / Berndt, L. / Weis, D.M. / Janetzky, M. / Zuehlke, D. ...Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoeker, O. / Wang, N. / Hocking, D. / Jebeli, L. / Girbardt, B. / Berndt, L. / Weis, D.M. / Janetzky, M. / Zuehlke, D. / Sievers, S. / Strugnell, R.A. / Olsen, C.A. / Hofmann, K. / Lammers, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9gkx.cif.gz | 413 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9gkx.ent.gz | 261.3 KB | Display | PDB format |
PDBx/mmJSON format | 9gkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9gkx_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 9gkx_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 9gkx_validation.xml.gz | 81.4 KB | Display | |
Data in CIF | 9gkx_validation.cif.gz | 115.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/9gkx ftp://data.pdbj.org/pub/pdb/validation_reports/gk/9gkx | HTTPS FTP |
-Related structure data
Related structure data | 9gkuC 9gkvC 9gkwC 9gkyC 9gkzC 9gl0C 9gl1C 9glbC 9gn1C 9gn6C 9gn7C 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40816.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: His6x-Tag fusion-protein / Source: (gene. exp.) Rhizorhabdus wittichii DC-6 (bacteria) / Strain: DC-6 / KACC 16600 / Gene: dmhA / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067XIQ6 |
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-Non-polymers , 5 types, 1792 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-K / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M Potassium fluoride pH 7.3 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 4, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 174428 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / CC1/2: 0.994 / Rrim(I) all: 0.229 / Rsym value: 0.21 / Χ2: 0.99 / Net I/σ(I): 7.68 |
Reflection shell | Resolution: 1.75→1.86 Å / Num. unique obs: 28058 / CC1/2: 0.488 / Χ2: 0.9 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.31 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.75→46.31 Å
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