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- PDB-3bac: Structural Basis for the Inhibition of Bacterial NAD+ Dependent D... -

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Basic information

Entry
Database: PDB / ID: 3bac
TitleStructural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase
ComponentsDNA ligase
KeywordsLIGASE / Adenylation Domain / DNA damage / DNA repair / DNA replication / NAD
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
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 / DNA ligase/mRNA capping enzyme / 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 / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3B9 / PHOSPHATE ION / DNA ligase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsPinko, C.
CitationJournal: To be Published
Title: Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase
Authors: Pinko, C. / Borchardt, A. / Nikulin, V. / Su, Y.
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)30,8575
Polymers30,1431
Non-polymers7134
Water27015
1
A: DNA ligase
hetero molecules

A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,71310
Polymers60,2872
Non-polymers1,4278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_885-y+3,-x+3,-z+2/31
Buried area7438 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.031, 95.031, 197.183
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 30143.256 Da / Num. of mol.: 1 / Fragment: Adenylation Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: ligN, lig / Production host: Escherichia coli (E. coli) / References: UniProt: P43813, DNA ligase (NAD+)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-3B9 / N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide


Mass: 428.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THAT THESE CONFLICTS ARE VARIANTS/CONFLICTS BETWEEN DIFFERENT REFERENCES.

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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: 4.26 Å3/Da / Density % sol: 71.15 %
Crystal growMethod: hanging drop / Details: hanging drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→24 Å / Num. obs: 10800 / Biso Wilson estimate: 107.7 Å2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
CNX2000.1refinement
RefinementResolution: 3→24 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 368416.406 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1114 10.3 %RANDOM
Rwork0.216 ---
obs-10800 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.731 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-5.11 Å219.83 Å20 Å2
2--5.11 Å20 Å2
3----10.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 47 15 2060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 190 11.5 %
Rwork0.333 1463 -
all-1653 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.paramprotein.top
X-RAY DIFFRACTION23235.param
X-RAY DIFFRACTION3po4.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION5protein_rep.param
X-RAY DIFFRACTION6water_rep.param
X-RAY DIFFRACTION73235.param
X-RAY DIFFRACTION8po4.param

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