+Open data
-Basic information
Entry | Database: PDB / ID: 8i86 | ||||||
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Title | Crystal structure of Cph001-D189N in complex with GTP | ||||||
Components | Viomycin kinase | ||||||
Keywords | TRANSFERASE / Phosphotransferase / Capreomycin / Cph / Resistance / GTP | ||||||
Function / homology | viomycin kinase / viomycin kinase activity / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / phosphorylation / Protein kinase-like domain superfamily / GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Viomycin kinase Function and homology information | ||||||
Biological species | Streptosporangium roseum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 | 8i86.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i86.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 8i86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i86_validation.pdf.gz | 760.5 KB | Display | wwPDB validaton report |
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Full document | 8i86_full_validation.pdf.gz | 764.4 KB | Display | |
Data in XML | 8i86_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 8i86_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i86 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i86 | HTTPS FTP |
-Related structure data
Related structure data | 8i80C 8i82C 8i84C 8i85C 8i89C 8i8gC 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: Chemical | ChemComp-PEG / | #3: Chemical | ChemComp-GTP / | #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: 2.56 Å3/Da / Density % sol: 51.9 % |
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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: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→30 Å / Num. obs: 29326 / % possible obs: 99.5 % / Redundancy: 3.81 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.03 |
Reflection shell | Resolution: 2.23→2.37 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 4318 / CC1/2: 0.924 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→28.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.991 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.251 / 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: 63.61 Å2
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Refinement step | Cycle: 1 / Resolution: 2.23→28.3 Å
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Refine LS restraints |
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