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- PDB-6kjm: Structural basis for domain rotation during adenylation of active... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kjm | ||||||
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Title | Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis | ||||||
![]() | DNA ligase A | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramachandran, R. / Shukla, A. / Afsar, M. | ||||||
![]() | ![]() Title: Structure based identification of first-in-class fragment inhibitors that target the NMN pocket of M. tuberculosis NAD + -dependent DNA ligase A. Authors: Shukla, A. / Afsar, M. / Kumar, N. / Kumar, S. / Ramachandran, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.5 KB | Display | ![]() |
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PDB format | ![]() | 102.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kkvC ![]() 6lw8C ![]() 1zauS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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: 37607.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: H37Rv / Gene: ligA / Production host: ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-NMN / ![]() | ||||
#3: Chemical | ChemComp-AMP / ![]() | ||||
#4: Chemical | ChemComp-SO4 / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.5 % |
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Crystal grow![]() | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1M HEPES Na pH=7.6 0.1M NaCl 1.5M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo condition / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 24, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→46.57 Å / Num. obs: 28579 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.041 / Rrim(I) all: 0.119 / Net I/σ(I): 15.9 / Num. measured all: 227755 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ZAU Resolution: 2.2→43.227 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.48 Å2 / Biso mean: 38.9705 Å2 / Biso min: 8.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→43.227 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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