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Yorodumi- PDB-6p08: Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p08 | |||||||||
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Title | Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate | |||||||||
Components | Kanamycin nucleotidyltransferase | |||||||||
Keywords | TRANSFERASE/ANTIBIOTIC / Aminoglycoside nucelotidyl transferase (ANT) / Aminoglycoside modifying enzymes (AGMEs) / DNA polymerase / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex | |||||||||
Function / homology | Function and homology information nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to antibiotic Similarity search - Function | |||||||||
Biological species | Bacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | |||||||||
Authors | Selvaraj, B. / Cuneo, M.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: "Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction Authors: Selvaraj, B. / Kocaman, S. / Trifas, M. / Serpersu, E.H. / Cuneo, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p08.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p08.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 6p08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p08_validation.pdf.gz | 508 KB | Display | wwPDB validaton report |
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Full document | 6p08_full_validation.pdf.gz | 512.3 KB | Display | |
Data in XML | 6p08_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 6p08_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/6p08 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p08 | HTTPS FTP |
-Related structure data
Related structure data | 6p01C 6p04C 6p06C 1knyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 29121.855 Da / Num. of mol.: 2 / Mutation: E52D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: knt, kan Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P05058, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 5 types, 238 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 8K, 0.1 M Tris pH 8.0, 0.1 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→49.65 Å / Num. obs: 30558 / % possible obs: 97.6 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.05 / Rrim(I) all: 0.134 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.27→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2512 / CC1/2: 0.919 / Rpim(I) all: 0.243 / Rrim(I) all: 0.476 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KNY Resolution: 2.27→49.65 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→49.65 Å
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Refine LS restraints |
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LS refinement shell |
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