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- PDB-8vdn: DNA Ligase 1 with nick dG:C -

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Basic information

Entry
Database: PDB / ID: 8vdn
TitleDNA Ligase 1 with nick dG:C
Components
  • DNA ligase 1
  • Downstream Oligo
  • Template Oligo
  • Upstream Oligo
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 ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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
DepositionDec 16, 2023Deposition 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
C: Downstream Oligo
B: Upstream Oligo
D: Template Oligo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3805
Polymers84,0324
Non-polymers3471
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-49 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.977, 115.631, 126.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 73042.258 Da / Num. of mol.: 1 / Fragment: UNP residues 261-918 / Mutation: E346A, E592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18858, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules CBD

#2: DNA chain Downstream Oligo


Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Upstream Oligo


Mass: 3405.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Template Oligo


Mass: 5446.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 39 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.: 38 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.4, 100 mM Lithium acetate, 12% w/v PEG 3350

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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: 2.39→40 Å / Num. obs: 38037 / % possible obs: 99.39 % / Redundancy: 6.5 % / Biso Wilson estimate: 66.84 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rpim(I) all: 0.031 / Net I/σ(I): 17.1
Reflection shellResolution: 2.39→2.44 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1880 / CC1/2: 0.673 / CC star: 0.897 / Rpim(I) all: 0.51 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→39.52 Å / SU ML: 0.3977 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0676
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 1987 5.25 %
Rwork0.2068 35856 -
obs0.2087 37843 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.23 Å2
Refinement stepCycle: LAST / Resolution: 2.39→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 732 23 38 5502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235653
X-RAY DIFFRACTIONf_angle_d0.55457842
X-RAY DIFFRACTIONf_chiral_restr0.0364898
X-RAY DIFFRACTIONf_plane_restr0.0046896
X-RAY DIFFRACTIONf_dihedral_angle_d18.57391042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.48211290.41042412X-RAY DIFFRACTION94.11
2.45-2.520.37661410.33992522X-RAY DIFFRACTION98.89
2.52-2.590.33691480.28782514X-RAY DIFFRACTION99.07
2.59-2.680.29911270.26672544X-RAY DIFFRACTION99.29
2.68-2.770.33831460.26442535X-RAY DIFFRACTION99.7
2.77-2.880.29121520.27222543X-RAY DIFFRACTION99.3
2.88-3.010.31151380.28852553X-RAY DIFFRACTION99.59
3.02-3.170.3271360.2742564X-RAY DIFFRACTION99.82
3.17-3.370.27691420.22932526X-RAY DIFFRACTION98.02
3.37-3.630.22981420.21282579X-RAY DIFFRACTION99.27
3.63-40.26271490.2142575X-RAY DIFFRACTION99.63
4-4.580.18821420.16542622X-RAY DIFFRACTION99.6
4.58-5.760.22461460.17182613X-RAY DIFFRACTION99.1
5.76-39.520.18451490.16692754X-RAY DIFFRACTION99.32
Refinement TLS params.Method: refined / Origin x: -5.29409465768 Å / Origin y: 13.6242548149 Å / Origin z: -30.931612066 Å
111213212223313233
T0.487958102606 Å20.0667588476911 Å20.0112085171344 Å2-0.294655922325 Å20.0128697577113 Å2--0.512477298794 Å2
L1.87239705571 °2-0.114595791972 °20.00917498750136 °2-3.0438278387 °20.268084534395 °2--3.36499033305 °2
S-0.0899780720625 Å °0.00409827488108 Å °0.0776857625178 Å °-0.547760467506 Å °0.0990739889139 Å °0.0878071718595 Å °-0.247069030721 Å °-0.155449698059 Å °-0.0222087909845 Å °
Refinement TLS groupSelection details: all

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