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Yorodumi- PDB-6kdu: Structural basis for domain rotation during adenylation of active... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kdu | ||||||
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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 | DNA BINDING PROTEIN / 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 H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ramachandran, R. / Shukla, A. / Afsar, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial ...Title: Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity. Authors: Afsar, M. / Shukla, A. / Kumar, N. / Ramachandran, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kdu.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kdu.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdu ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdu | HTTPS FTP |
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-Related structure data
Related structure data | 6krhC 6kscC 6ksdC 1zauS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36846.125 Da / Num. of mol.: 1 / Mutation: E22A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: ligA / Plasmid: pQE60 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WNV1, DNA ligase (NAD+) | ||||
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#2: Chemical | ChemComp-AMP / | ||||
#3: Chemical | ChemComp-NMN / | ||||
#4: Chemical | #5: 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: 3.64 Å3/Da / Density % sol: 66.25 % |
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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 1.5 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo conditions / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9784 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 14, 2019 / Details: Cilindrical Mirror with 50 nm Pt-coating | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si111 with LN2 closed loop cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.084 Å / Num. obs: 28776 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.017 / Rrim(I) all: 0.074 / Net I/σ(I): 32.4 | ||||||||||||||||||||||||||||||
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: 2.2→48.084 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.66 Å2 / Biso mean: 48.723 Å2 / Biso min: 18.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.084 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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