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

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Basic information

Entry
Database: PDB / ID: 6kjm
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: 2.2 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 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 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

Downloads & links

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Assembly

Deposited unit
A: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6757
Polymers37,6081
Non-polymers1,0676
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size exclusion chromatography using superdex 200 10/300 GL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.728, 95.728, 201.347
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: 37607.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: ligA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WNV1, DNA ligase (NAD+)
#2: 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
#3: 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
#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.: 105 / 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: 3.78 Å3/Da / Density % sol: 67.5 %
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 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: 2.2→46.57 Å / Num. obs: 28579 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.041 / Rrim(I) all: 0.119 / Net I/σ(I): 15.9 / Num. measured all: 227755 / Scaling rejects: 2
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
2.2-2.278.10.8791964524200.790.3230.9392.7100
9.07-46.576.30.026319951110.010.02847.599

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Processing

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

1zau


Resolution: 2.2→43.227 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2462 1418 4.98 %
Rwork0.216 --
obs0.2175 28493 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.48 Å2 / Biso mean: 38.9705 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 2.2→43.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 91 112 2681
Biso mean--52.47 36.1 -
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
2.2001-2.27870.28981200.25752680
2.2787-2.370.30051410.24162629
2.37-2.47780.25851390.2352649
2.4778-2.60840.25941380.22622652
2.6084-2.77180.26611540.22032651
2.7718-2.98580.24521370.22962691
2.9858-3.28620.3091560.22882686
3.2862-3.76140.23961320.20342727
3.7614-4.73810.21321400.17922773
4.7381-43.2270.21961610.22852937

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