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Yorodumi- PDB-8vxb: Structure of ANT(6)-Ib from Campylobacter fetus subsp fetus compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vxb | ||||||
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Title | Structure of ANT(6)-Ib from Campylobacter fetus subsp fetus complexed with hydrated streptomycin | ||||||
Components | Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib | ||||||
Keywords | TRANSFERASE / Campylobacter / streptomycin / antibiotic resistance | ||||||
Function / homology | Aminoglycoside 6-adenylyltransferase / Streptomycin adenylyltransferase / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / Chem-5I0 / PHOSPHATE ION / Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib Function and homology information | ||||||
Biological species | Campylobacter fetus subsp. fetus (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Nalam, P. / Cook, P. / Smith, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2024 Title: Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)-Ib From Campylobacter fetus subsp. fetus. Authors: Nalam, P. / Cook, P.D. / Smith, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vxb.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vxb.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 8vxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vxb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8vxb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8vxb_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8vxb_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/8vxb ftp://data.pdbj.org/pub/pdb/validation_reports/vx/8vxb | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 36517.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter fetus subsp. fetus (Campylobacter) Gene: ant(6)-Ib / Production host: Escherichia coli (E. coli) / References: UniProt: D8L9Z0 |
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#2: Chemical | ChemComp-5I0 / [( |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium malate, 10 % PEG 3350, 10 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979493 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 9, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979493 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→127.57 Å / Num. obs: 34637 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.076 / Rrim(I) all: 0.347 / Net I/σ(I): 10.6 / Num. measured all: 708684 |
Reflection shell | Resolution: 1.85→1.95 Å / % possible obs: 100 % / Redundancy: 21.1 % / Rmerge(I) obs: 4.272 / Num. measured all: 104983 / Num. unique obs: 4977 / CC1/2: 0.513 / Rpim(I) all: 0.945 / Rrim(I) all: 4.376 / Net I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→45 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→45 Å
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Refine LS restraints |
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LS refinement shell |
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