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- PDB-5fpr: Structure of Bacterial DNA Ligase with small-molecule ligand pyri... -

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Basic information

Entry
Database: PDB / ID: 5fpr
TitleStructure of Bacterial DNA Ligase with small-molecule ligand pyrimidin-2-amine (AT371) in an alternate binding site.
ComponentsDNA LIGASE
KeywordsLIGASE / ANTIBIOTIC DESIGN / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT371.
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA replication / DNA repair / DNA binding / metal ion binding / cytosol
Similarity search - Function
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 ...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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / D-amino Acid Aminotransferase; Chain A, domain 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
PYRIMIDIN-2-AMINE / DNA ligase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJhoti, H. / Ludlow, R.F. / Pathuri, P. / Saini, H.K. / Tickle, I.J. / Tisi, D. / Verdonk, M. / Williams, P.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening.
Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H.
#1: Journal: Acs Med.Chem.Lett. / Year: 2013
Title: Fragment-Based Discovery of 6-Azaindazoles as Inhibitors of Bacterial DNA Ligase.
Authors: Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, ...Authors: Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, F. / Mccloskey, L. / Mortenson, P.N. / Pathuri, P. / Tisi, D. / Williams, P.A.
History
DepositionDec 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0124
Polymers36,7251
Non-polymers2873
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.871, 39.290, 48.645
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2325-

HOH

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Components

#1: Protein DNA LIGASE / POLYDEOXYRIBONUCLEOTIDE SYNTHASE NAD(+)


Mass: 36724.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9AIU7, DNA ligase (NAD+), DNA ligase (ATP)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-LGA / PYRIMIDIN-2-AMINE


Mass: 95.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRIMIDIN-2-AMINE (L01): ASTEX COMPOUND REGISTRY AT371.

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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: 2.36 Å3/Da / Density % sol: 47.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0 Å / Relative weight: 1
ReflectionResolution: 2→85.9 Å / Num. obs: 22674 / % possible obs: 98.6 % / Observed criterion σ(I): -3.7 / Redundancy: 3.4 % / Biso Wilson estimate: 23.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CC5

4cc5


Resolution: 2→85.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9197 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1151 5.24 %RANDOM
Rwork0.1531 ---
obs0.1561 21955 98.3 %-
Displacement parametersBiso mean: 28.17 Å2
Baniso -1Baniso -2Baniso -3
1-5.4428 Å20 Å21.0741 Å2
2---6.6831 Å20 Å2
3---1.2403 Å2
Refine analyzeLuzzati coordinate error obs: 0.185 Å
Refinement stepCycle: LAST / Resolution: 2→85.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 17 510 2959
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112501HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973387HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d881SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes366HARMONIC16
X-RAY DIFFRACTIONt_it2501HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.79
X-RAY DIFFRACTIONt_other_torsion16.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion317SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3270SEMIHARMONIC4
LS refinement shellResolution: 2→2.1 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2086 149 5.05 %
Rwork0.1456 2802 -
all0.1488 2951 -
obs--99.73 %
Refinement TLS params.

T13: -0.0202 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.21290.16490.0160.7421-0.30720.8943-0.0191-0.13580.053-0.03270.01590.0015-0.0287-0.00920.0033-0.00960.00650.0035-0.0221-0.047510.004717.952938.2101
21.1390.4643-0.58980.5323-0.30261.50810.0131-0.06220.0319-0.0113-0.00980.0063-0.00660.1763-0.0033-0.07250.0253-0.0457-0.0177-0.050725.977818.338214.9058

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