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- PDB-8u6x: ATP-dependent DNA ligase Lig E from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 8u6x
TitleATP-dependent DNA ligase Lig E from Neisseria gonorrhoeae
Components
  • DNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
  • DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
  • DNA ligase
KeywordsLIGASE/DNA / enzyme-adenylate / Lig E / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / THIOCYANATE ION / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae MS11 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsWilliamson, A. / Pan, J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)21/754 New Zealand
CitationJournal: Bmc Microbiol. / Year: 2024
Title: A role for the ATP-dependent DNA ligase lig E of Neisseria gonorrhoeae in biofilm formation.
Authors: Pan, J. / Singh, A. / Hanning, K. / Hicks, J. / Williamson, A.
History
DepositionSep 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase
B: DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4377
Polymers44,9163
Non-polymers5214
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.398, 167.680, 51.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA ligase


Mass: 32029.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae MS11 (bacteria) / Gene: NGFG_01849 / Plasmid: pDEST 17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: D6HB39

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')


Mass: 6494.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')


Mass: 6392.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 46 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 59.1 % / Description: small rods/ plates
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.5 M potassium thiocyanate, 0.1 M Bis Tris Propane pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 2.44→48.93 Å / Num. obs: 13286 / % possible obs: 99.86 % / Redundancy: 8.7 % / Biso Wilson estimate: 53.06 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1076 / Rpim(I) all: 0.03774 / Rrim(I) all: 0.1144 / Net I/σ(I): 11.88
Reflection shellResolution: 2.44→2.527 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 1269 / CC1/2: 0.694 / CC star: 0.905 / Rpim(I) all: 0.3757 / Rrim(I) all: 1.146 / % possible all: 99.61

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→48.93 Å / SU ML: 0.3919 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2795 1329 10.01 %
Rwork0.2295 11954 -
obs0.2346 13283 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.64 Å2
Refinement stepCycle: LAST / Resolution: 2.44→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 246 31 42 2295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272328
X-RAY DIFFRACTIONf_angle_d0.51363180
X-RAY DIFFRACTIONf_chiral_restr0.0406326
X-RAY DIFFRACTIONf_plane_restr0.0034372
X-RAY DIFFRACTIONf_dihedral_angle_d18.1688403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.540.38151400.33731265X-RAY DIFFRACTION98.8
2.54-2.650.35751460.29281302X-RAY DIFFRACTION99.72
2.65-2.790.38371440.2751298X-RAY DIFFRACTION100
2.79-2.970.32591450.27521304X-RAY DIFFRACTION100
2.97-3.190.35431480.29411329X-RAY DIFFRACTION99.93
3.2-3.520.34351450.22841316X-RAY DIFFRACTION99.86
3.52-4.030.27351490.22351338X-RAY DIFFRACTION99.93
4.03-5.070.19181500.1781356X-RAY DIFFRACTION100
5.07-48.930.25161620.21381446X-RAY DIFFRACTION99.81

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