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- PDB-1m4i: Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tubercul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m4i | ||||||
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Title | Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis-Complex with Coenzyme A and Kanamycin A | ||||||
![]() | Aminoglycoside 2'-N-acetyltransferase | ||||||
![]() | TRANSFERASE / COA BINDING MOTIF | ||||||
Function / homology | ![]() aminoglycoside 2'-N-acetyltransferase activity / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vetting, M.W. / Hegde, S.S. / Javid-Majd, F. / Blanchard, J.S. / Roderick, S.L. | ||||||
![]() | ![]() Title: Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis in complex with coenzyme A and aminoglycoside substrates. Authors: Vetting, M.W. / Hegde, S.S. / Javid-Majd, F. / Blanchard, J.S. / Roderick, S.L. #1: ![]() Title: Overexpression and Mechanistic Analysis of Chromosomally Encoded Aminoglycoside 2'-N-Acetyltransferase (AAC(2')-Ic) from Mycobacterium tuberculosis Authors: Hegde, S.S. / Javid-Majd, F. / Blanchard, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 73 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m44SC ![]() 1m4dC ![]() 1m4gC 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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Details | The biological assembly is a dimer, as contained in the assymetric unit |
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Components
#1: Protein | Mass: 20063.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5N0, UniProt: P9WQG9*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PAP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium Sulfate, ADA, Coenzyme A, Kanamycin A, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2002 / Details: Confocal mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 62335 / Num. obs: 62335 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 23.7 Å2 / Rsym value: 0.031 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 7109 / Rsym value: 0.11 / % possible all: 85.25 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 62407 / Rmerge(I) obs: 0.031 |
Reflection shell | *PLUS % possible obs: 84.1 % / Rmerge(I) obs: 0.11 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1M44 Resolution: 1.5→24.09 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.147 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→24.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.179 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.338 / Rfactor Rwork: 0.31 |