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- PDB-7sx5: Crystal structure of ligase I with nick duplexes containing misma... -

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Basic information

Entry
Database: PDB / ID: 7sx5
TitleCrystal structure of ligase I with nick duplexes containing mismatch A:C
Components
  • DNA chain 1
  • DNA chain 2
  • DNA chain 3
  • DNA ligase 1
KeywordsLIGASE / Protein-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 replication, damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / : / Processive synthesis on the lagging strand / Processive synthesis on the C-strand of the telomere / lagging strand elongation / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) ...Okazaki fragment processing involved in mitotic DNA replication / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / : / Processive synthesis on the lagging strand / Processive synthesis on the C-strand of the telomere / lagging strand elongation / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / PCNA-Dependent Long Patch Base Excision Repair / 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 ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, Q. / Gulkis, M. / McKenna, R. / Caglayan, M.
Funding support1items
OrganizationGrant numberCountry
Other privateUniversity of Florida Thomas H. Maren Junior Investigator Fund P0158597
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 22, 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

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Assembly

Deposited unit
A: DNA ligase 1
B: DNA chain 1
C: DNA chain 2
D: DNA chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6485
Polymers85,3014
Non-polymers3471
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-48 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.755, 116.407, 126.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 74326.656 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 chain 1


Mass: 3389.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA chain 2


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


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, 183 molecules

#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100 mM MES pH 6.6, 100 mM lithium acetate, 20% (w/v) polyethylene glycol 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: 2.8→20 Å / Num. obs: 36695 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.947 / CC star: 0.986 / Net I/σ(I): 21.2
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 1273 / CC1/2: 0.707 / CC star: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SUM

7sum


Resolution: 2.8→19.96 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 1974 5.38 %
Rwork0.1752 34721 -
obs0.1772 36695 82.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.38 Å2 / Biso mean: 38.3039 Å2 / Biso min: 4.71 Å2
Refinement stepCycle: final / Resolution: 2.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 731 22 182 5835
Biso mean--31.86 29.7 -
Num. residues----672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.3563750.28931131120638
2.87-2.950.3015820.26211505158750
2.95-3.030.24491080.24311737184559
3.03-3.130.26851210.21552087220870
3.13-3.240.19851140.19962338245277
3.24-3.370.21131240.19722572269685
3.37-3.520.23621410.19412801294292
3.52-3.710.21541130.17922967308098
3.71-3.940.20181810.16482956313799
3.94-4.240.19682260.15112929315599
4.24-4.660.14521890.14162830301995
4.66-5.330.21781650.15852874303996
5.33-6.670.22741860.1829903176100
6.67-19.960.23161490.15863004315399

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