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- PDB-5fpo: Structure of Bacterial DNA Ligase with small-molecule ligand 1H- ... -

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Basic information

Entry
Database: PDB / ID: 5fpo
TitleStructure of Bacterial DNA Ligase with small-molecule ligand 1H- indazol-7-amine (AT4213) in an alternate binding site.
ComponentsDNA LIGASE
KeywordsLIGASE / ANTIBIOTIC DESIGN / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT4213.
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 / Dna Ligase; domain 1 - #70 / 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 ...Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / Dna Ligase; domain 1 - #70 / 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
1H-indazol-7-amine / DNA ligase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 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)37,1244
Polymers36,7251
Non-polymers3993
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.886, 39.660, 48.780
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2029-

HOH

21A-2032-

HOH

31A-2059-

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-10L / 1H-indazol-7-amine


Mass: 133.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H7N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1H-INDAZOL-7-AMINE (10L): ASTEX COMPOUND REGISTRY AT4213.
Sequence detailsDELETION 313-355 C-TERM HIS TAG.

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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: 2.43 Å3/Da / Density % sol: 48.96 % / Description: NONE
Crystal growDetails: 1.6M (NH4)2SO4. PROTEIN CONC. = 27.2 MG/ML.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.83→48.8 Å / Num. obs: 29257 / % possible obs: 96.7 % / Observed criterion σ(I): -3.7 / Redundancy: 2.3 % / Biso Wilson estimate: 21.58 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.4
Reflection shellResolution: 1.83→1.92 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / % possible all: 89.3

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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: 1.83→48.78 Å / Cor.coef. Fo:Fc: 0.8799 / Cor.coef. Fo:Fc free: 0.8891 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.141 / Details: DISORDERED REGIONS WERE DELETED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1486 5.25 %RANDOM
Rwork0.2114 ---
obs0.2133 28309 96.33 %-
Displacement parametersBiso mean: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.9045 Å20 Å2-0.4158 Å2
2---5.0087 Å20 Å2
3---2.1042 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 1.83→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 30 231 2651
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112491HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993386HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d856SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes368HARMONIC16
X-RAY DIFFRACTIONt_it2491HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.98
X-RAY DIFFRACTIONt_other_torsion15.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion319SEMIHARMONIC5
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_contact3077SEMIHARMONIC4
LS refinement shellResolution: 1.83→1.9 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.273 117 4.48 %
Rwork0.2246 2496 -
all0.2267 2613 -
obs--85.42 %
Refinement TLS params.

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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71420.3786-0.24721.0141-0.02941.1675-0.0089-0.04570.06170.0035-0.0679-0.02330.0119-0.04420.0768-0.1022-0.0132-0.01730.10330.0115-0.06210.051818.141738.024
21.770.4848-0.53990.5188-0.10751.0723-0.0289-0.05580.0298-0.03620.05260.0467-0.0568-0.1328-0.0237-0.09520.0241-0.0121-0.05620.0121-0.038425.973718.409915.1726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|3 - A|60 }
2X-RAY DIFFRACTION2{ A|61 - A|309 }

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