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- PDB-6ras: Pmar-Lig_Pre. -

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Basic information

Entry
Database: PDB / ID: 6ras
TitlePmar-Lig_Pre.
Components
  • ATP-dependent DNA ligase
  • DNA
  • DNA (5'-D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
  • DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
KeywordsDNA BINDING PROTEIN / DNA ligase / ATP-dependent / ligase-DNA co-crystal structure / determinants in DNA binding
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding / metal ion binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / : / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / ATP-dependent DNA ligase
Similarity search - Component
Biological speciesProchlorococcus marinus str. MIT 9302 (bacteria)
DNA launch vector pDE-GFP2 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLeiros, H.K.S. / Williamson, A.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway Norway
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
Authors: Williamson, A. / Leiros, H.S.
History
DepositionApr 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
C: DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
D: DNA
I: ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5839
Polymers63,7434
Non-polymers8405
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-71 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.469, 103.408, 68.906
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain DNA (5'-D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')


Mass: 6479.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)
#2: DNA chain DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')


Mass: 3035.007 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: There is a break in the chain between nt31 and nt32.
Source: (synth.) DNA launch vector pDE-GFP2 (others)
#3: DNA chain DNA


Mass: 3342.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)

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Protein , 1 types, 1 molecules I

#4: Protein ATP-dependent DNA ligase


Mass: 50886.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a R120 A mutant
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9302 (bacteria)
Gene: EU96_0746 / Production host: Prochlorococcus marinus (bacteria) / References: UniProt: A0A0A2ACP7

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Non-polymers , 4 types, 201 molecules

#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG, buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.69→25 Å / Num. obs: 24531 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.089 / Net I/av σ(I): 9.5 / Net I/σ(I): 9.5
Reflection shellResolution: 2.69→2.82 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3459 / CC1/2: 0.475 / Rpim(I) all: 0.602 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Home-made

Resolution: 2.75→24.366 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 1227 5.01 %
Rwork0.1876 --
obs0.1904 24493 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→24.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 857 52 196 4592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174588
X-RAY DIFFRACTIONf_angle_d1.3296337
X-RAY DIFFRACTIONf_dihedral_angle_d13.5232606
X-RAY DIFFRACTIONf_chiral_restr0.067685
X-RAY DIFFRACTIONf_plane_restr0.006658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.35581390.29682553X-RAY DIFFRACTION99
2.86-2.98990.36231590.2762549X-RAY DIFFRACTION100
2.9899-3.14720.3139900.23552637X-RAY DIFFRACTION100
3.1472-3.34390.26021430.21742568X-RAY DIFFRACTION99
3.3439-3.60140.28041170.18882580X-RAY DIFFRACTION99
3.6014-3.96240.22681410.16962595X-RAY DIFFRACTION100
3.9624-4.53260.21671360.15162582X-RAY DIFFRACTION99
4.5326-5.69850.20111420.15252593X-RAY DIFFRACTION99
5.6985-24.36710.20771600.18282609X-RAY DIFFRACTION99

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