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

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Basic information

Entry
Database: PDB / ID: 6krh
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 / 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 / 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 / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 21, 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)37,9967
Polymers36,9291
Non-polymers1,0676
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer when purified by using Superdex 200 10/300 GL (GE Healthcare)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-60 kcal/mol
Surface area16050 Å2
Unit cell
Length a, b, c (Å)95.549, 95.549, 200.589
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: 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+)
#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.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.74 Å3/Da / Density % sol: 67.08 %
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 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 25, 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: 2.6→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 shellResolution: 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

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Processing

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

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
RfactorNum. reflection% reflection
Rfree0.264 880 5.06 %
Rwork0.224 16508 -
obs0.226 17388 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.34 Å2 / Biso mean: 50.71 Å2 / Biso min: 14.55 Å2
Refinement stepCycle: final / Resolution: 2.6→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 91 43 2640
Biso mean--69.73 39.86 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.76290.29041380.239326612799
2.7629-2.97620.32141410.253927042845
2.9762-3.27560.30991470.250126902837
3.2756-3.74930.26971420.226327322874
3.7493-4.72280.22791490.188527782927
4.7228-43.130.24741630.227929433106

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