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

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Basic information

Entry
Database: PDB / ID: 6kdu
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
KeywordsDNA BINDING PROTEIN / Ligase
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / peptidoglycan-based cell wall / DNA replication / DNA repair / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
DNA ligase-like, N-terminal NAD+-binding domain / 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 ...DNA ligase-like, N-terminal NAD+-binding domain / 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 / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRamachandran, R. / Shukla, A. / Afsar, M.
CitationJournal: 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
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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)37,8176
Polymers36,8461
Non-polymers9715
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-14 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.168, 96.168, 200.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-601-

HOH

31A-603-

HOH

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Components

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


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+)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo conditions / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9784 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 14, 2019 / Details: Cilindrical Mirror with 50 nm Pt-coating
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2716.40.9394004724390.8990.2380.9693.6100
9.07-48.0814.30.021746852210.0060.02210299.4

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Processing

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

1zau


Resolution: 2.2→48.084 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.11
RfactorNum. reflection% reflection
Rfree0.2445 1420 4.95 %
Rwork0.2097 --
obs0.2114 28693 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.66 Å2 / Biso mean: 48.723 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 2.2→48.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 86 103 2683
Biso mean--72.29 42.76 -
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
2.2-2.27860.28551410.25842657
2.2786-2.36990.28791390.22692658
2.3699-2.47770.28651330.22172684
2.4777-2.60840.26351360.2262676
2.6084-2.77180.29171450.2262683
2.7718-2.98570.25561380.23772693
2.9857-3.28610.31751400.23882716
3.2861-3.76150.24211370.20592749
3.7615-4.73840.20041480.17132792
4.7384-48.0840.21821630.20632965

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