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- PDB-8vzm: DNA Ligase 1 captured with pre-step 3 ligation at the rA:T nicksite -

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Basic information

Entry
Database: PDB / ID: 8vzm
TitleDNA Ligase 1 captured with pre-step 3 ligation at the rA:T nicksite
Components
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
  • DNA ligase 1
  • DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*A)-3')
KeywordsLigase/DNA / LIG1 / DNA Ligase 1 / LIGASE / Ligase-DNA complex
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation ...Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mismatch repair / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA recombination / cell division / intracellular membrane-bounded organelle / DNA repair / mitochondrion / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. ...DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / 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 / DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKanalElamparithi, B. / Gulkis, M. / Caglayan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147111-02 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA.
Authors: Balu, K.E. / Gulkis, M. / Almohdar, D. / Caglayan, M.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase 1
B: DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*A)-3')
D: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6795
Polymers85,3324
Non-polymers3471
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-48 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.844, 115.961, 123.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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DNA chain , 2 types, 2 molecules DC

#3: DNA chain DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5461.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')


Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AB

#1: Protein DNA ligase 1 / / DNA ligase I / Polydeoxyribonucleotide synthase [ATP] 1


Mass: 74326.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Organ: 9606 / Cell (production host): Escherichia coli BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18858, DNA ligase (ATP)
#2: DNA/RNA hybrid DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*A)-3')


Mass: 3405.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 149 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 298.1 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100 mM MES (pH 6.7), 100 mM lithium acetate, 16% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25.06 Å / Num. obs: 32094 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 60 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.04 / Net I/σ(I): 27.3
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1562 / CC1/2: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→25.06 Å / SU ML: 0.3215 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 2012 6.28 %
Rwork0.1795 30013 -
obs0.1828 32025 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.54 Å2
Refinement stepCycle: LAST / Resolution: 2.51→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 733 23 148 5814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245854
X-RAY DIFFRACTIONf_angle_d0.54238102
X-RAY DIFFRACTIONf_chiral_restr0.0361923
X-RAY DIFFRACTIONf_plane_restr0.0051928
X-RAY DIFFRACTIONf_dihedral_angle_d18.79051059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.30831410.26471969X-RAY DIFFRACTION93.16
2.57-2.640.30941450.25982097X-RAY DIFFRACTION99.73
2.64-2.720.31591300.25852140X-RAY DIFFRACTION99.3
2.72-2.810.33691460.26622133X-RAY DIFFRACTION99.69
2.81-2.910.34781410.2532131X-RAY DIFFRACTION99.78
2.91-3.030.28771460.24072148X-RAY DIFFRACTION99.83
3.03-3.160.26451400.22992139X-RAY DIFFRACTION99.56
3.16-3.330.25861320.20992105X-RAY DIFFRACTION97.9
3.33-3.540.24341510.17942135X-RAY DIFFRACTION98.88
3.54-3.810.24891460.18412152X-RAY DIFFRACTION99.57
3.81-4.190.22941430.15912153X-RAY DIFFRACTION99.44
4.19-4.790.17681470.14042196X-RAY DIFFRACTION99.83
4.79-6.030.221510.15852216X-RAY DIFFRACTION99.92
6.03-25.060.18211530.14442299X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: -5.40166688042 Å / Origin y: 12.7001922607 Å / Origin z: -31.5158123135 Å
111213212223313233
T0.382772102033 Å2-0.0144902840479 Å2-0.0956672819056 Å2-0.281349938078 Å2-0.00275310360904 Å2--0.464088650378 Å2
L1.69155579628 °2-0.303583238179 °2-0.0022262352778 °2-2.21524275398 °20.698060252149 °2--2.4471225036 °2
S-0.069208462999 Å °-0.0481375488211 Å °0.140844020653 Å °-0.22300952841 Å °-0.0312879425782 Å °0.363893515595 Å °-0.145619812144 Å °-0.166253294109 Å °0.0699023309373 Å °
Refinement TLS groupSelection details: all

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