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- PDB-6p0b: Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy ... -

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Basic information

Entry
Database: PDB / ID: 6p0b
TitleHuman DNA Ligase 1 (E346A/E592A) 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 / protein-DNA complex / phosphotransferase / OB fold / DNA Binding domain / Adenylation Domain / metalloenzyme
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 / 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) ...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 / 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) / 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: 2.203 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.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)83,21110
Polymers82,6604
Non-polymers5516
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-74 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.866, 101.398, 115.606
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: 71669.938 Da / Num. of mol.: 1 / Fragment: residues 262-904 / Mutation: E346A, E592A
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, 392 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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.: 386 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 43118 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.77 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.051 / Rrim(I) all: 0.119 / Χ2: 1.021 / Net I/σ(I): 6.2 / Num. measured all: 227628
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.41.24542450.5220.5911.3811.00299.7
2.28-2.375.10.91942380.6640.4451.0240.9999.4
2.37-2.484.60.67242610.7130.3490.761199.3
2.48-2.615.70.55542500.8480.2550.6121.0299.8
2.61-2.775.60.38542960.9260.1770.4251.01799.9
2.77-2.995.50.26342900.9630.1230.2911.049100
2.99-3.295.20.13343260.9950.0640.1481.0399.9
3.29-3.764.90.07343090.9970.0360.0821.0198.9
3.76-4.745.70.04943600.9980.0220.0541.04199.9
4.74-505.10.0445430.9990.0190.0451.0498.9

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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: 2.203→41.428 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2056 2169 5.04 %
Rwork0.1699 --
obs0.1717 43011 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 274.83 Å2 / Biso mean: 54.7983 Å2 / Biso min: 20.06 Å2
Refinement stepCycle: final / Resolution: 2.203→41.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 731 46 387 6178
Biso mean--46.59 48.57 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056022
X-RAY DIFFRACTIONf_angle_d0.738323
X-RAY DIFFRACTIONf_chiral_restr0.044935
X-RAY DIFFRACTIONf_plane_restr0.005946
X-RAY DIFFRACTIONf_dihedral_angle_d16.9493546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2032-2.25440.31541190.27372539265893
2.2544-2.31080.28751250.256127362861100
2.3108-2.37330.28371430.2452663280699
2.3733-2.44310.28541450.23322703284899
2.4431-2.52190.27091580.22727102868100
2.5219-2.61210.30491430.215726862829100
2.6121-2.71660.24361330.20427442877100
2.7166-2.84020.26171420.200827302872100
2.8402-2.98990.25411640.203727152879100
2.9899-3.17720.21221380.19327302868100
3.1772-3.42240.20951430.17482693283697
3.4224-3.76660.17521530.15362742289599
3.7666-4.31110.1781460.13127562902100
4.3111-5.42970.16071720.119627912963100
5.4297-41.43490.17061450.14922904304999
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)
11.27560.1678-0.7710.90860.3561.15210.1078-0.11910.18150.099-0.0493-0.045-0.22330.0625-00.315-0.04110.0010.3093-0.02120.36233.013811.8852-7.0273
20.70030.64070.09380.7468-0.29940.7549-0.16330.1332-0.1575-0.22330.0393-0.13750.17810.13700.34990.0130.0610.35120.02010.376739.1163-4.2532-24.9434
31.6119-0.3015-0.56572.24070.23161.53750.00080.1293-0.0288-0.0870.03030.10470.0411-0.1660.00010.30660.00280.02080.2862-0.00160.3315.8769-23.024-16.4885
40.6926-0.01150.21940.30460.09550.58340.02340.0382-0.0127-0.083-0.10330.0060.0089-0.1581-00.32520.02740.07060.33930.02980.43541.34091.6794-11.9773
51.6926-0.3433-0.16231.03280.60290.51360.06280.00270.12710.07310.00210.2346-0.0036-0.250300.30830.02390.02380.35720.00220.3388-4.81392.9256-4.8642
60.1806-0.01920.27320.002-0.02960.35970.1653-0.1475-0.12380.01140.3008-0.2138-0.1181-0.07370.00430.3875-0.0054-0.00340.3909-0.04940.30716.2522-5.63185.6208
70.26230.47240.15630.87230.40890.37990.11040.44280.13020.30460.42050.34090.00650.13580.3780.33830.03150.03730.33660.00950.341911.60182.9141-21.1314
80.1451-0.0315-0.00730.0236-0.01160.01090.02680.08640.097-0.00810.08540.12880.1572-0.0907-00.4029-0.0280.00730.3633-0.00860.331216.98422.3965-19.9449
90.18090.1750.1290.16840.09640.0960.0924-0.02260.01480.154-0.02190.0089-0.05160.0809-00.43020.04160.02340.3942-0.02510.286615.2927-4.3597.5234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 261 through 455 )A261 - 455
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 544 )A456 - 544
3X-RAY DIFFRACTION3chain 'A' and (resid 545 through 741 )A545 - 741
4X-RAY DIFFRACTION4chain 'A' and (resid 742 through 784 )A742 - 784
5X-RAY DIFFRACTION5chain 'A' and (resid 785 through 901 )A785 - 901
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 13 )B3 - 13
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 7 )C1 - 7
8X-RAY DIFFRACTION8chain 'D' and (resid 9 through 15 )D9 - 15
9X-RAY DIFFRACTION9chain 'D' and (resid 16 through 26 )D16 - 26

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