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- PDB-6sxj: Crystal structure of spectinomycin adenyltransferase AAD(9) from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sxj | |||||||||
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Title | Crystal structure of spectinomycin adenyltransferase AAD(9) from Enterococcus faecialis | |||||||||
![]() | Streptomycin 3''-adenylyltransferase | |||||||||
![]() | TRANSFERASE / nucleotidyltransferase / antibiotic resistance | |||||||||
Function / homology | Adenylyltransferase AadA, C-terminal domain / Aminoglycoside adenylyltransferase, C-terminal domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / response to antibiotic / ATP binding / Spectinomycin 9-adenylyltransferase![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kanchugal P, S. / Selmer, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Recognition of Spectinomycin by Resistance Enzyme ANT(9) from Enterococcus faecalis. Authors: Kanchugal P, S. / Selmer, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
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Full document | ![]() | 439.3 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xxqC ![]() 6xz0C ![]() 5g4aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 30873.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q07448, streptomycin 3''-adenylyltransferase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % / Description: Hexagonal prism shaped |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M of each aminoacid, 0.1 M bicine/Trizma base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37 Å / Num. obs: 18995 / % possible obs: 99 % / Redundancy: 13.7 % / Biso Wilson estimate: 51.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.058 / Net I/σ(I): 1.5 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1843 / CC1/2: 0.8 / Rpim(I) all: 0.4 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G4A Resolution: 2.1→36.98 Å / SU ML: 0.296 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3315
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.98 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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