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Yorodumi- PDB-8i8g: Crystal structure of Cph001-D189N in complex with CMN IIA and ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i8g | ||||||
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Title | Crystal structure of Cph001-D189N in complex with CMN IIA and ATP | ||||||
Components |
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Keywords | TRANSFERASE / Phosphotransferase / Capreomycin / Cph / Resistance / ATP | ||||||
Function / homology | viomycin kinase / viomycin kinase activity / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / phosphorylation / Protein kinase-like domain superfamily / Capreomycin IA / ADENOSINE-5'-TRIPHOSPHATE / Viomycin kinase Function and homology information | ||||||
Biological species | Streptosporangium roseum (bacteria) Saccharothrix mutabilis subsp. capreolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Chang, C.Y. / Toh, S.I. / Elaine K, J. / Hsiao, P.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin. Authors: Toh, S.I. / Elaine Keisha, J. / Wang, Y.L. / Pan, Y.C. / Jhu, Y.H. / Hsiao, P.Y. / Liao, W.T. / Chen, P.Y. / Ko, T.M. / Chang, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i8g.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i8g.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 8i8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i8g_validation.pdf.gz | 737.8 KB | Display | wwPDB validaton report |
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Full document | 8i8g_full_validation.pdf.gz | 739.1 KB | Display | |
Data in XML | 8i8g_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 8i8g_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i8g ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i8g | HTTPS FTP |
-Related structure data
Related structure data | 8i80C 8i82C 8i84C 8i85C 8i86C 8i89C 8i8hC 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: 30438.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptosporangium roseum (bacteria) / Gene: Sros_4606 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2B3F1 #2: Protein/peptide | | Type: Cyclic peptide / Class: Inhibitor / Mass: 686.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CMN IIA Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria) Production host: Saccharothrix mutabilis subsp. capreolus (bacteria) References: Capreomycin IA #3: Chemical | ChemComp-ATP / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Sodium acetate trihydrate, Polyethylene glycol 4,000, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 13117 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1286 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→26.18 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / 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: 59.332 Å2
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Refinement step | Cycle: 1 / Resolution: 3→26.18 Å
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Refine LS restraints |
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