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Yorodumi- PDB-6kkv: Structural basis for domain rotation during adenylation of active... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kkv | ||||||
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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 | ||||||
Components | DNA ligase A | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA ligation / peptidoglycan-based cell wall / DNA replication / magnesium ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Ramachandran, R. / Shukla, A. / Afsar, M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kkv.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kkv.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kkv_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6kkv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6kkv_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6kkv_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/6kkv ftp://data.pdbj.org/pub/pdb/validation_reports/kk/6kkv | HTTPS FTP |
-Related structure data
Related structure data | 6kjmC 6lw8C 1zauS 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
#1: Protein | Mass: 36904.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ligA, lig, Rv3014c, MTV012.28c / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P9WNV1, DNA ligase (NAD+) | ||||
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#2: Chemical | ChemComp-DKR / | ||||
#3: Chemical | #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: 3.75 Å3/Da / Density % sol: 67.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1 M HEPES pH 7.6 0.1 M NaCl 1.5 M 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: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
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: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.56→47.7 Å / Num. obs: 18263 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.041 / Rrim(I) all: 0.14 / Net I/σ(I): 17.7 / Num. measured all: 209155 / Scaling rejects: 11 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZAU Resolution: 2.56→43.104 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 189.45 Å2 / Biso mean: 51.3752 Å2 / Biso min: 13.28 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.56→43.104 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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