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- PDB-3pn1: Novel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad S... -

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Basic information

Entry
Database: PDB / ID: 3pn1
TitleNovel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad Spectrum Potency and Antibacterial Efficacy In Vivo
ComponentsDNA ligase
KeywordsLigase/Ligase Inhibitor / ATP grasp fold / ligase / DNA / bacteria / Ligase-Ligase Inhibitor complex
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / DNA binding / metal ion binding / cytosol
Similarity search - Function
DNA ligase-like, N-terminal NAD+-binding domain / Dna Ligase; domain 1 - #70 / 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 ...DNA ligase-like, N-terminal NAD+-binding domain / Dna Ligase; domain 1 - #70 / 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 / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Dna Ligase; domain 1 / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-(butylsulfanyl)adenosine / Chem-IWH / DNA ligase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMills, S. / Eakin, A. / Buurman, E. / Newman, J. / Gao, N. / Huynh, H. / Johnson, K. / Lahiri, S. / Shapiro, A. / Walkup, G. ...Mills, S. / Eakin, A. / Buurman, E. / Newman, J. / Gao, N. / Huynh, H. / Johnson, K. / Lahiri, S. / Shapiro, A. / Walkup, G. / Wei, Y. / Stokes, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2011
Title: Novel Bacterial NAD+-Dependent DNA Ligase Inhibitors with Broad-Spectrum Activity and Antibacterial Efficacy In Vivo.
Authors: Mills, S.D. / Eakin, A.E. / Buurman, E.T. / Newman, J.V. / Gao, N. / Huynh, H. / Johnson, K.D. / Lahiri, S. / Shapiro, A.B. / Walkup, G.K. / Yang, W. / Stokes, S.S.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4113
Polymers35,8001
Non-polymers6122
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.806, 137.806, 56.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA ligase / Polydeoxyribonucleotide synthase [NAD+]


Mass: 35799.574 Da / Num. of mol.: 1 / Fragment: Adenylation Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: ligA, lig, ligN, HI_1100 / Production host: Escherichia coli (E. coli) / References: UniProt: P43813, DNA ligase (NAD+)
#2: Chemical ChemComp-IVH / 2-(butylsulfanyl)adenosine


Mass: 355.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N5O4S
#3: Chemical ChemComp-IWH / 1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide


Mass: 256.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 16% (w/v) polyethylene glycol (PEG) 3500, 350mM sodium potassium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→25.95 Å / Num. obs: 36612 / % possible obs: 99 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.95 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.456 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1827 5 %RANDOM
Rwork0.2014 ---
obs0.2029 36612 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.95 Å2 / Biso mean: 27.4439 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→25.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 43 215 2773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222616
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9923560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13324.048126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17115428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7981521
X-RAY DIFFRACTIONr_chiral_restr0.1430.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212020
X-RAY DIFFRACTIONr_mcbond_it1.2691.51591
X-RAY DIFFRACTIONr_mcangle_it2.17522573
X-RAY DIFFRACTIONr_scbond_it3.38631025
X-RAY DIFFRACTIONr_scangle_it5.2144.5987
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 127 -
Rwork0.296 2467 -
all-2594 -
obs--97.34 %

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