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Yorodumi- PDB-6krh: Structural basis for domain rotation during adenylation of active... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6krh | ||||||
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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 H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 6krh.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6krh.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 6krh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6krh_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6krh_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6krh_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6krh_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6krh ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6krh | HTTPS FTP |
-Related structure data
Related structure data | 6kduC 6kscC 6ksdC 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: 36929.188 Da / Num. of mol.: 1 / Mutation: H236Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: 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-AMP / | ||||
#3: Chemical | ChemComp-NMN / | ||||
#4: Chemical | ChemComp-SO4 / #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: 3.74 Å3/Da / Density % sol: 67.08 % |
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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: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 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: 2.6→47.77 Å / Num. obs: 17451 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.045 / Rrim(I) all: 0.147 / Net I/σ(I): 17.7 / Num. measured all: 184962 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.898 / Num. measured all: 22503 / Num. unique obs: 2073 / CC1/2: 0.852 / Rpim(I) all: 0.285 / Rrim(I) all: 0.943 / Net I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZAU Resolution: 2.6→43.13 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 210.34 Å2 / Biso mean: 50.71 Å2 / Biso min: 14.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→43.13 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %
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