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- PDB-9bs3: Wild type DNA Ligase 1 with 5'-rG:C -

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Basic information

Entry
Database: PDB / ID: 9bs3
TitleWild type DNA Ligase 1 with 5'-rG:C
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
  • DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA ligase 1
  • DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
KeywordsLIGASE/DNA / DNA binding protein / DNA repair / BER / Human DNA Ligase 1 / LIGASE-DNA complex
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / 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) ...Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / 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 / nucleus / metal ion binding
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 ...: / 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 ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKanalElamparithi, B. / Caglayan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM14711101 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair.
Authors: Balu, K.E. / Tang, Q. / Almohdar, D. / Ratcliffe, J. / Kalaycioglu, M. / Caglayan, M.
History
DepositionMay 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 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 (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
C: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
E: DNA ligase 1
F: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
G: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
H: DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,10310
Polymers165,4088
Non-polymers6942
Water2,522140
1
A: DNA ligase 1
B: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
C: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0515
Polymers82,7044
Non-polymers3471
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-46 kcal/mol
Surface area31340 Å2
MethodPISA
2
E: DNA ligase 1
F: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3')
G: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')
H: DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0515
Polymers82,7044
Non-polymers3471
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-36 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.348, 117.287, 104.048
Angle α, β, γ (deg.)90.000, 98.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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DNA chain , 2 types, 4 molecules BFDH

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


Mass: 3405.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5446.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA/RNA hybrid , 2 types, 4 molecules AECG

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


Mass: 71697.992 Da / Num. of mol.: 2
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)
#3: DNA/RNA hybrid DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')


Mass: 2154.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 142 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.52 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion
Details: 100mM MES pH 5.3, 18% PEG3350, 100mM Lithium Acetate.

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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: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→25 Å / Num. obs: 45825 / % possible obs: 97.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 46.82 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.074 / Rrim(I) all: 0.184 / Net I/σ(I): 13
Reflection shellResolution: 2.69→2.75 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2314 / CC1/2: 0.811 / Rpim(I) all: 0.313 / Rrim(I) all: 0.809

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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: 2.69→24.86 Å / SU ML: 0.3388 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.6812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1998 4.4 %
Rwork0.2078 43427 -
obs0.2096 45425 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.85 Å2
Refinement stepCycle: LAST / Resolution: 2.69→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8572 1471 44 140 10227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003110445
X-RAY DIFFRACTIONf_angle_d0.556714472
X-RAY DIFFRACTIONf_chiral_restr0.03811654
X-RAY DIFFRACTIONf_plane_restr0.00411619
X-RAY DIFFRACTIONf_dihedral_angle_d21.39024007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.750.34921300.29732835X-RAY DIFFRACTION86.62
2.75-2.830.32111430.27563099X-RAY DIFFRACTION97.68
2.83-2.910.26691440.25593108X-RAY DIFFRACTION96.7
2.91-30.28321410.25363079X-RAY DIFFRACTION95.8
3-3.110.31391460.25083172X-RAY DIFFRACTION98.87
3.11-3.240.30711470.24993191X-RAY DIFFRACTION98.64
3.24-3.380.28641450.21843159X-RAY DIFFRACTION98.63
3.38-3.560.26341450.21343189X-RAY DIFFRACTION98.84
3.56-3.780.23951460.20073166X-RAY DIFFRACTION98.42
3.78-4.070.22591450.1953143X-RAY DIFFRACTION97.92
4.07-4.480.23151360.17942961X-RAY DIFFRACTION91.2
4.48-5.120.22591420.18413081X-RAY DIFFRACTION95.21
5.12-6.440.2231430.19873117X-RAY DIFFRACTION96.19
6.44-24.860.20261450.17173127X-RAY DIFFRACTION94.79
Refinement TLS params.Method: refined / Origin x: 10.7062335441 Å / Origin y: -24.9226112305 Å / Origin z: 2.08224008966 Å
111213212223313233
T0.301711863746 Å2-0.0129877431904 Å20.0052294526876 Å2-0.293906193595 Å20.00117316635569 Å2--0.247948651088 Å2
L0.334067187934 °2-0.0032119455436 °2-0.0683798505998 °2-0.377501633768 °2-0.107079171872 °2--0.12169831067 °2
S-0.0129359764443 Å °0.0321757077719 Å °0.0309766427014 Å °-0.048054222464 Å °-0.007586377132 Å °-0.041935521223 Å °-0.0151062448051 Å °0.0319044981447 Å °0.0179400683807 Å °
Refinement TLS groupSelection details: all

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