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

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Basic information

Entry
Database: PDB / ID: 6ksc
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


base-excision repair, DNA ligation / DNA ligase (NAD+) / DNA ligase (NAD+) activity / 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
ADENOSINE MONOPHOSPHATE / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 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)37,4724
Polymers36,9321
Non-polymers5393
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, purified as a monomer from the size exclusion chromatography using superdex 200 10/300 GL column (GE Healthcare).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-31 kcal/mol
Surface area15760 Å2
Unit cell
Length a, b, c (Å)95.290, 95.290, 201.879
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: 36932.172 Da / Num. of mol.: 1 / Mutation: K123R
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+)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / 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-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.: 22 / 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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1M HEPES Na pH=7.6 0.1M NaCl 1.5M 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: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 2019
RadiationMonochromator: Water-cooled DCM with Si (111) or Si(220) crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→47.65 Å / Num. obs: 21664 / % possible obs: 99.1 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Net I/σ(I): 14.5 / Num. measured all: 246998 / Scaling rejects: 164
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
2.4-2.4911.90.9942665022320.7770.2981.042.399.8
8.98-47.659.30.018434746810.0060.0229.593.2

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZAU

1zau


Resolution: 2.4→36.268 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.19
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.3082 1078 4.98 %
Rwork0.2699 --
obs0.2719 21646 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.87 Å2 / Biso mean: 73.2304 Å2 / Biso min: 28.31 Å2
Refinement stepCycle: final / Resolution: 2.4→36.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 45 23 2490
Biso mean--74.68 49.45 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.50940.44981300.3852546100
2.5094-2.64160.41261370.3658251199
2.6416-2.80710.35871290.3396255499
2.8071-3.02370.40541280.3292252999
3.0237-3.32780.38321440.3119254599
3.3278-3.80890.2941410.2751256798
3.8089-4.79710.25311400.2249258598
4.7971-36.2680.26831290.2326273196

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