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- PDB-7sum: Crystal structure of human ligase I with nick duplexes containing... -

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Basic information

Entry
Database: PDB / ID: 7sum
TitleCrystal structure of human ligase I with nick duplexes containing cognate A:T
Components
  • DNA ligase 1
  • DNA(5'-*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*A-3')
  • DNA(5'-*GP*TP*CP*CP*GP*AP*CP*TP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C-3')
  • DNA(5'-P*GP*TP*CP*GP*GP*AP*C-3')
KeywordsLIGASE/DNA / 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 / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Processive synthesis on the C-strand of the telomere ...Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Processive synthesis on the C-strand of the telomere / 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 / DNA repair / intracellular membrane-bounded organelle / 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / 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: 2.9 Å
AuthorsTang, Q. / Gulkis, M. / McKenna, R. / Caglayan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Florida Thomas H. Maren Junior Investigator FundP0158597 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair.
Authors: Tang, Q. / Gulkis, M. / McKenna, R. / Caglayan, M.
History
DepositionNov 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 21, 2022Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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'-*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*A-3')
C: DNA(5'-P*GP*TP*CP*GP*GP*AP*C-3')
D: DNA(5'-*GP*TP*CP*CP*GP*AP*CP*TP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3795
Polymers84,0314
Non-polymers3471
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-47 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.255, 116.589, 124.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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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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
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 BCD

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


Mass: 3389.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA(5'-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)
#4: DNA chain DNA(5'-*GP*TP*CP*CP*GP*AP*CP*TP*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)

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Non-polymers , 2 types, 141 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 21707 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Net I/σ(I): 2.8
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 1042 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6P0D

6p0d


Resolution: 2.9→19.93 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1132 5.34 %
Rwork0.18 --
obs0.183 21183 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.89 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 733 22 140 5858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.29321200.27962232X-RAY DIFFRACTION89
3.03-3.190.30551510.25932436X-RAY DIFFRACTION97
3.19-3.390.30481560.21432474X-RAY DIFFRACTION99
3.39-3.650.22531230.1912546X-RAY DIFFRACTION100
3.65-4.010.24731320.18422540X-RAY DIFFRACTION100
4.01-4.590.18861760.15132524X-RAY DIFFRACTION100
4.59-5.760.20341260.15272604X-RAY DIFFRACTION100
5.76-19.930.19431480.15922695X-RAY DIFFRACTION100

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