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- PDB-6p0c: Human DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DN... -

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Basic information

Entry
Database: PDB / ID: 6p0c
TitleHuman DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DNA nick in EDTA
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 / protein-DNA complex / phosphotransferase / OB fold / DNA Binding domain / Adenylation Domain / metalloenzyme / 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 / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / mismatch repair / anatomical structure morphogenesis / 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 i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / 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/mRNA capping enzyme ...DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / 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/mRNA capping enzyme / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchellenberg, M.J. / Tumbale, P.S. / Riccio, A.A. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nat Commun / Year: 2019
Title: Two-tiered enforcement of high-fidelity DNA ligation.
Authors: Tumbale, P.P. / Jurkiw, T.J. / Schellenberg, M.J. / Riccio, A.A. / O'Brien, P.J. / Williams, R.S.
History
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)83,2537
Polymers82,7764
Non-polymers4763
Water20,0691114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-48 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.235, 101.322, 115.319
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: 71786.016 Da / Num. of mol.: 1 / Fragment: residues 262-904
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Plasmid: pMCSG7 / 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.) synthetic construct (others)
#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.) synthetic construct (others)
#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.) synthetic construct (others)

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Non-polymers , 4 types, 1117 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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES, 100 mM Lithium Acetate, 15% (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: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 120809 / % possible obs: 97.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Rrim(I) all: 0.119 / Χ2: 1.01 / Net I/σ(I): 8.6 / Num. measured all: 831310
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.616.11.932109340.4960.8372.1120.88889.6
1.61-1.676.71.295118550.7920.5411.4070.93597.3
1.67-1.756.70.86119590.8890.3590.9340.98897.8
1.75-1.846.70.601120430.9040.250.6531.03498.1
1.84-1.956.70.38120560.950.1580.4131.09398.4
1.95-2.16.80.237121050.9740.0980.2571.05598.6
2.1-2.327.10.165122770.9860.0670.1791.03199.5
2.32-2.657.40.122123250.990.0480.131199.8
2.65-3.347.40.085124400.9950.0340.0921.01399.8
3.34-507.10.063128150.9960.0250.0681.0399.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X9N

1x9n


Resolution: 1.55→33.602 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.33
RfactorNum. reflection% reflection
Rfree0.1653 6040 5.02 %
Rwork0.1304 --
obs0.1322 120366 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117 Å2 / Biso mean: 30.8197 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.55→33.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 733 52 1115 6922
Biso mean--32.14 44.17 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066134
X-RAY DIFFRACTIONf_angle_d0.8388490
X-RAY DIFFRACTIONf_chiral_restr0.049956
X-RAY DIFFRACTIONf_plane_restr0.006979
X-RAY DIFFRACTIONf_dihedral_angle_d16.5393685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5415-1.5590.36771320.33092605273767
1.559-1.57730.32252030.27313772397597
1.5773-1.59650.2781970.25743735393297
1.5965-1.61680.26952060.2373736394297
1.6168-1.6380.23771830.21633746392997
1.638-1.66050.24532220.19573733395597
1.6605-1.68420.2351850.1853782396798
1.6842-1.70930.23322020.18193794399697
1.7093-1.7360.22011980.16533760395897
1.736-1.76450.20381950.15973821401698
1.7645-1.79490.2042020.15613781398398
1.7949-1.82760.20492000.14193814401498
1.8276-1.86270.19492050.13513779398498
1.8627-1.90070.1832010.13493848404998
1.9007-1.9420.18842080.13483826403498
1.942-1.98720.18761930.12063824401798
1.9872-2.03690.15842040.11663838404299
2.0369-2.0920.16181980.11093844404299
2.092-2.15350.17412100.11023877408799
2.1535-2.2230.15531900.10933880407099
2.223-2.30240.1451780.106739364114100
2.3024-2.39460.16761940.105838914085100
2.3946-2.50360.15112400.10938584098100
2.5036-2.63550.15372030.111439424145100
2.6355-2.80060.15971840.118739294113100
2.8006-3.01670.16562350.127539394174100
3.0167-3.320.14442110.12413906411799
3.32-3.79980.13262100.118139744184100
3.7998-4.78520.12682210.111240174238100
4.7852-33.60980.17182300.14724139436999

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