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- PDB-6gdr: DNA binding with a minimal scaffold: Structure-function analysis ... -

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Basic information

Entry
Database: PDB / ID: 6gdr
TitleDNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases
Components
  • DNA
  • DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
  • DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
  • DNA ligase
KeywordsLIGASE / DNA ligases
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA repair / ATP binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesAlteromonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWilliamson, A. / Grigic, M. / Leiros, H.K.S.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway244247 Norway
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.
Authors: Williamson, A. / Grgic, M. / Leiros, H.S.
History
DepositionApr 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
C: DNA
D: DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3967
Polymers45,8594
Non-polymers5373
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: have done MicroScale Thermophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-45 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.024, 71.207, 117.160
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number5
Space group name H-MI121

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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*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')


Mass: 6494.194 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA


Mass: 3004.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')


Mass: 3342.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Production host: Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules A

#4: Protein DNA ligase


Mass: 33017.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Gene: BM525_03130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0SCU0

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Non-polymers , 3 types, 72 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 24% PEG 4K, 100 mM Bis-Tris pH 5.5, 12% ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.33→47.92 Å / Num. obs: 22739 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 39.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Net I/σ(I): 14.6
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2184 / CC1/2: 0.493 / Rpim(I) all: 0.0858 / Rrim(I) all: 1.635 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.33→24.84 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.17
RfactorNum. reflection% reflection
Rfree0.2641 1143 5.03 %
Rwork0.2181 --
obs0.2205 22708 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.33→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 856 32 69 2988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033090
X-RAY DIFFRACTIONf_angle_d0.5564350
X-RAY DIFFRACTIONf_dihedral_angle_d19.8291661
X-RAY DIFFRACTIONf_chiral_restr0.04469
X-RAY DIFFRACTIONf_plane_restr0.002405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3272-2.4330.33231470.30382629X-RAY DIFFRACTION97
2.433-2.56120.34331490.3152702X-RAY DIFFRACTION100
2.5612-2.72150.36391410.31952669X-RAY DIFFRACTION98
2.7215-2.93130.40081210.30672727X-RAY DIFFRACTION100
2.9313-3.22570.29921430.2642707X-RAY DIFFRACTION99
3.2257-3.69120.27911530.22112665X-RAY DIFFRACTION98
3.6912-4.64550.26091430.1792718X-RAY DIFFRACTION99
4.6455-24.84090.18681460.17122748X-RAY DIFFRACTION98

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