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- PDB-7l35: Human DNA Ligase 1 - R771W nicked DNA complex -

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Basic information

Entry
Database: PDB / ID: 7l35
TitleHuman DNA Ligase 1 - R771W nicked DNA complex
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*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
KeywordsLIGASE/DNA / DNA ligase / 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 / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTumbale, P.P. / Williams, R.S. / Schellenberg, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01ES102765 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency.
Authors: Jurkiw, T.J. / Tumbale, P.P. / Schellenberg, M.J. / Cunningham-Rundles, C. / Williams, R.S. / O'Brien, P.J.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)83,6468
Polymers83,0474
Non-polymers5984
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-54 kcal/mol
Surface area30010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.330, 100.523, 116.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 72057.258 Da / Num. of mol.: 1 / Mutation: R771W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18858, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules BCD

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


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5486.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 609 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6, 100 mM lithium acetate, 15% (w/v) polyethylene glycol 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: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57075 / % possible obs: 99.87 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 1.046 / Num. unique obs: 5634 / CC1/2: 0.763

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P0A

6p0a


Resolution: 2→38.732 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 2870 5.03 %
Rwork0.1626 54166 -
obs0.1643 57036 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.21 Å2 / Biso mean: 40.6345 Å2 / Biso min: 13.48 Å2
Refinement stepCycle: final / Resolution: 2→38.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 732 73 608 6359
Biso mean--36.28 45.38 -
Num. residues----670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036153
X-RAY DIFFRACTIONf_angle_d0.6368542
X-RAY DIFFRACTIONf_chiral_restr0.042959
X-RAY DIFFRACTIONf_plane_restr0.004964
X-RAY DIFFRACTIONf_dihedral_angle_d17.3173667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03280.24341360.21722552100
2.0328-2.06780.24661320.20052539100
2.0678-2.10540.23251400.20372559100
2.1054-2.14590.23971410.19352529100
2.1459-2.18970.22841250.19712576100
2.1897-2.23730.28271260.1872544100
2.2373-2.28940.23461080.18972582100
2.2894-2.34660.23561340.17882547100
2.3466-2.41010.19681390.16452550100
2.4101-2.4810.21131590.16572555100
2.481-2.5610.21381300.16812562100
2.561-2.65260.18861320.16562580100
2.6526-2.75870.22351270.17422556100
2.7587-2.88430.22131420.1732573100
2.8843-3.03630.22851450.17962579100
3.0363-3.22640.18991330.17292588100
3.2264-3.47540.19151410.1487256899
3.4754-3.82480.13941360.14612607100
3.8248-4.37760.17221440.12892632100
4.3776-5.51280.17261640.13652631100
5.5128-38.7320.17981360.1684275799
Refinement TLS params.Method: refined / Origin x: 18.7467 Å / Origin y: -3.7421 Å / Origin z: -11.6878 Å
111213212223313233
T0.1345 Å20.0201 Å2-0.0011 Å2-0.1206 Å20.0052 Å2--0.1064 Å2
L0.8784 °20.1214 °2-0.28 °2-0.5853 °2-0.1068 °2--0.5883 °2
S0.0255 Å °0.0013 Å °0.0704 Å °0.0228 Å °-0.0073 Å °0.0558 Å °-0.076 Å °-0.0362 Å °-0.0116 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA260 - 901
2X-RAY DIFFRACTION1allB3 - 13
3X-RAY DIFFRACTION1allC1 - 7
4X-RAY DIFFRACTION1allD9 - 26
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allS1 - 828
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allH1

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