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- PDB-6p09: Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA... -

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Basic information

Entry
Database: PDB / ID: 6p09
TitleHuman DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+
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 / 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 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 / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase AMP-binding site. ...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 / DNA ligase/mRNA capping enzyme / 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 / 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: 2.052 Å
AuthorsSchellenberg, M.J. / Williams, R.S. / Tumbale, P.S. / Riccio, A.A.
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 / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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)83,35111
Polymers82,7764
Non-polymers5757
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-79 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.039, 101.083, 115.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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, 569 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES, 100 mM Lithium Acetate, 15% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99203 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99203 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 53293 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 33.93 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.098 / Χ2: 1.02 / Net I/σ(I): 7.8 / Num. measured all: 388082
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.05-2.126.551290.510.6041.20297.4
2.12-2.217.452570.7220.3630.961000.934
2.21-2.317.452840.8430.2710.9841000.6960.747
2.31-2.437.452710.9060.1981.0011000.5080.545
2.43-2.587.453210.9480.1411.0161000.3630.39
2.58-2.787.452930.9780.0941.041000.2410.259
2.78-3.067.453320.9910.0581.0231000.150.161
3.06-3.517.453590.9980.0311000.0750.081
3.51-4.427.354160.9980.0231.0161000.0580.062
4.42-50756310.9990.0180.99499.80.0440.047

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xn9

1xn9


Resolution: 2.052→36.02 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 2673 5.03 %
Rwork0.17 --
obs0.1717 53178 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.052→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 731 35 562 6350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016077
X-RAY DIFFRACTIONf_angle_d0.8048354
X-RAY DIFFRACTIONf_dihedral_angle_d18.463588
X-RAY DIFFRACTIONf_chiral_restr0.047936
X-RAY DIFFRACTIONf_plane_restr0.005960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0524-2.08970.33571310.32022460X-RAY DIFFRACTION94
2.0897-2.12990.31721380.28142622X-RAY DIFFRACTION99
2.1299-2.17330.27681400.23342651X-RAY DIFFRACTION100
2.1733-2.22060.28411320.23152632X-RAY DIFFRACTION100
2.2206-2.27220.28561180.22222638X-RAY DIFFRACTION100
2.2722-2.3290.26871170.20262677X-RAY DIFFRACTION100
2.329-2.3920.25711420.19562648X-RAY DIFFRACTION100
2.392-2.46240.22631600.18432611X-RAY DIFFRACTION100
2.4624-2.54180.25041530.18562622X-RAY DIFFRACTION100
2.5418-2.63270.22791380.17532662X-RAY DIFFRACTION100
2.6327-2.7380.21451260.17242682X-RAY DIFFRACTION100
2.738-2.86260.20691450.18362631X-RAY DIFFRACTION100
2.8626-3.01340.2221480.18582680X-RAY DIFFRACTION100
3.0134-3.20210.221420.18372660X-RAY DIFFRACTION100
3.2021-3.44920.20081400.15972670X-RAY DIFFRACTION99
3.4492-3.7960.1611450.15442678X-RAY DIFFRACTION100
3.796-4.34440.16241470.13232696X-RAY DIFFRACTION100
4.3444-5.47040.16641680.12792730X-RAY DIFFRACTION100
5.4704-36.0250.16471430.15952855X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.60880.2944-0.33261.8546-0.5942.43310.1372-0.23190.28510.2911-0.07310.019-0.352-0.0612-0.06710.3189-0.04020.00670.2851-0.05560.333133.10211.7682-6.9646
22.03831.4761-1.10312.4905-1.41811.9268-0.13990.1016-0.073-0.21060.0081-0.32040.1680.25120.14080.29690.01860.06030.2884-0.02370.315139.1135-4.2268-25.0199
32.0836-0.3451-0.80622.38980.29352.8831-0.03210.1237-0.1043-0.06240.05210.15520.0543-0.2248-0.01970.2338-0.01340.03310.19180.00610.275715.8968-22.8682-16.4276
42.8307-1.5832-2.0251.14781.08261.60260.03350.20130.0497-0.075-0.21080.257-0.0759-0.27560.1750.31430.0687-0.01080.30120.08040.31171.361.7304-12.0081
52.86360.0678-1.00962.8556-0.35162.79940.13020.0130.27810.05890.04980.3292-0.1897-0.3056-0.16720.22980.04070.02950.28650.00050.3092-4.77862.9764-5.0436
60.3274-0.10531.07210.2692-0.40364.66370.1246-0.2611-0.04590.38530.1878-0.1484-0.2523-0.6871-0.29330.37430.05940.02460.4424-0.0130.248816.1445-4.98067.244
73.14860.9401-1.43091.3929-0.85073.2239-0.04240.28640.15430.21520.2731-0.0692-0.07150.073-0.26370.3170.02610.01620.25980.00170.249611.6843.0525-21.2171
83.0363-0.0405-1.02841.0885-0.11843.2437-0.13590.1901-0.02660.02040.14580.2480.4290.0932-0.04890.2958-0.00070.00640.2417-0.00210.269117.05082.567-20.0344
90.4534-0.25360.97950.3227-0.36412.2789-0.0588-0.03470.02960.26230.0140.0287-0.2880.21880.03050.37550.0210.01470.36160.00240.245715.6151-4.30697.4707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 455 )
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 544 )
3X-RAY DIFFRACTION3chain 'A' and (resid 545 through 741 )
4X-RAY DIFFRACTION4chain 'A' and (resid 742 through 784 )
5X-RAY DIFFRACTION5chain 'A' and (resid 785 through 901 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 13 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 7 )
8X-RAY DIFFRACTION8chain 'D' and (resid 9 through 15 )
9X-RAY DIFFRACTION9chain 'D' and (resid 16 through 26 )

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