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- PDB-6lw8: Structural basis for domain rotation during adenylation of active... -

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Basic information

Entry
Database: PDB / ID: 6lw8
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
Chem-EWO / DNA ligase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsRamachandran, R. / Afsar, M. / Shukla, A.
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
DepositionFeb 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)38,4949
Polymers37,6081
Non-polymers8868
Water41423
1
A: DNA ligase A
hetero molecules

A: DNA ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,98718
Polymers75,2162
Non-polymers1,77116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area5240 Å2
ΔGint-187 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.390, 95.390, 201.683
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-616-

HOH

21A-618-

HOH

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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 (bacteria) / Strain (production host): BL21 / References: UniProt: P9WNV1, DNA ligase (NAD+)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EWO / (4R)-4-(4-fluorophenyl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine


Mass: 217.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12FN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.6 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1M HEPES Na 0.1M NaCl 1.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 298 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: Dec 10, 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: 2.4→47.7 Å / Num. obs: 22031 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.013 / Rrim(I) all: 0.045 / Net I/σ(I): 38.2 / Num. measured all: 274459
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
2.4-2.4912.90.6512885922340.9180.1860.6784.299.5
8.98-47.79.40.016489852310.0060.017101.598.9

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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: 2.401→43.116 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1091 4.97 %
Rwork0.2393 20871 -
obs0.2408 21962 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.23 Å2 / Biso mean: 65.828 Å2 / Biso min: 20.99 Å2
Refinement stepCycle: final / Resolution: 2.401→43.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 72 23 2544
Biso mean--87.55 50.6 -
Num. residues----320
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4011-2.51030.35411300.30592548
2.5103-2.64270.35421350.28712529
2.6427-2.80820.32161310.27412571
2.8082-3.0250.34071310.28822552
3.025-3.32930.32681440.26772579
3.3293-3.81080.25211450.23722602
3.8108-4.80020.22671430.19752650
4.8002-43.10.24771320.23332840

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