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- PDB-2owo: Last Stop on the Road to Repair: Structure of E.coli DNA Ligase B... -

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Basic information

Entry
Database: PDB / ID: 2owo
TitleLast Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate
Components
  • 26-MER
  • 5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
  • 5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'
  • DNA ligase
KeywordsLIGASE/DNA / DNA / Ligase / Protein-DNA complex / LIGASE-DNA COMPLEX
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA ligation / NAD+ binding / DNA replication / DNA binding / metal ion binding / cytosol
Similarity search - Function
Laminin - #30 / Laminin / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / Dna Ligase; domain 1 - #70 / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase ...Laminin - #30 / Laminin / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / Dna Ligase; domain 1 - #70 / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / Other non-globular / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShuman, S. / Nandakumar, J. / Nair, P.A.
CitationJournal: Mol.Cell / Year: 2007
Title: Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate.
Authors: Nandakumar, J. / Nair, P.A. / Shuman, S.
History
DepositionFeb 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 26-MER
C: 5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
D: 5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45710
Polymers89,6604
Non-polymers7976
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.441, 99.273, 86.245
Angle α, β, γ (deg.)90.000, 105.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

DetailsBiological assembly is a monomer

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain 26-MER


Mass: 8034.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#2: DNA chain 5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'


Mass: 3950.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: DNA chain 5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized

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Protein , 1 types, 1 molecules A

#4: Protein DNA ligase / Polydeoxyribonucleotide synthase [NAD+]


Mass: 73699.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ligA / Plasmid: pET-LigA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15042, DNA ligase (NAD+)

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Non-polymers , 4 types, 326 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: EcoLigA (0.3 mM) was reacted with 5 mM MgCl2 and 0.3 mM NAD+ for 30 min at 22 C. The ligase-adenylylation reaction was then quenched by adding 10 mM EDTA. The mixture was supplemented with ...Details: EcoLigA (0.3 mM) was reacted with 5 mM MgCl2 and 0.3 mM NAD+ for 30 min at 22 C. The ligase-adenylylation reaction was then quenched by adding 10 mM EDTA. The mixture was supplemented with 26-bp nicked duplex DNA (0.318 mM). This LigA-nucleic acid solution was mixed 1:2 with a well solution containing 200 mM ammonium sulfate, 50 mM sodium acetate, 24% PEG-4000. Crystals were grown at 22 C by the sitting drop vapor diffusion method. Crystals appeared after 3 days. The crystals were transferred serially to solutions containing 5% glycerol/24% PEG-4000, 10% glycerol/26% PEG-4000, 15% glycerol/28% PEG-4000, and 20% glycerol/30% PEG-4000 in 100 mM ammonium sulfate, 50 mM sodium acetate, after which they were flash-frozen in liquid nitrogen. , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2ammonium sulfate11
3PEG-40011
4sodium acetate12
5ammonium sulfate12
6PEG-40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 39615 / Num. obs: 39100 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.084 / Χ2: 1.503 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.422 / Num. unique all: 3598 / Χ2: 1.103 / % possible all: 91.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1. EfaLigA (aa 71-317 from PDB 1TA8) 2. TfiLigA (aa 433-584 and 321-391 from PDB 1V9P)

1ta8

1v9p


Resolution: 2.3→30.34 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1955275.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1959 5 %RANDOM
Rwork0.217 ---
all-39734 --
obs-39098 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.033 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å20 Å24.85 Å2
2---0.38 Å20 Å2
3---3.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 1062 44 320 5991
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 303 5.2 %
Rwork0.286 5573 -
obs-5876 88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna-apc_rep.paramdna-rna-apc.top
X-RAY DIFFRACTION2protein_rep-apl.paramprotein-apl.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.paramwater.top

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