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- PDB-6kkv: Structural basis for domain rotation during adenylation of active... -

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Basic information

Entry
Database: PDB / ID: 6kkv
TitleStructural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis
ComponentsDNA ligase A
KeywordsLIGASE
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
Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal ...Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-DKR / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsRamachandran, R. / Shukla, A. / Afsar, M.
CitationJournal: 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
DepositionJul 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3114
Polymers36,9041
Non-polymers4063
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer when purified by size exclusion chromatography using Superdex200 10/300 GL column (GE healthcare)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.402, 95.402, 201.281
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA ligase A / LigA / Polydeoxyribonucleotide synthase [NAD(+)]


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+)
#2: Chemical ChemComp-DKR / N-[(4-methylphenyl)methyl]-1H-pyrrole-2-carboxamide


Mass: 214.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo condition / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 24, 2019
RadiationMonochromator: Double crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.56-2.6711.80.9932562321650.8510.2991.0382.9100
8.87-47.790.03248135360.9990.0110.03446.598.6

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZAU

1zau


Resolution: 2.56→43.104 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.77
RfactorNum. reflection% reflection
Rfree0.2778 871 4.79 %
Rwork0.2318 --
obs0.234 18196 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 189.45 Å2 / Biso mean: 51.3752 Å2 / Biso min: 13.28 Å2
Refinement stepCycle: final / Resolution: 2.56→43.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 39 33 2564
Biso mean--62.41 38.13 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5601-2.72040.38191390.28482817
2.7204-2.93040.34571700.27462783
2.9304-3.22520.31811490.26522836
3.2252-3.69170.29351490.21922854
3.6917-4.65030.2381170.19772934
4.6503-43.1040.23441470.23163101

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