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- PDB-6rau: PostS3_Pmar_lig4_WT -

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Basic information

Entry
Database: PDB / ID: 6rau
TitlePostS3_Pmar_lig4_WT
Components
  • ATP-dependent DNA ligase
  • DNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
  • 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')
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 / DNA / DNA (> 10) / ATP-dependent DNA ligase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
DNA launch vector pDE-GFP2 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLeiros, H.K.S. / Williamson, A.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway0000 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 8, 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
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*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')
I: ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4807
Polymers63,8443
Non-polymers6354
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-93 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.725, 102.497, 68.356
Angle α, β, γ (deg.)90.00, 91.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules BC

#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 (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')


Mass: 6392.151 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

#3: Protein ATP-dependent DNA ligase


Mass: 50972.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Gene: EU96_0746 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A2ACP7

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Non-polymers , 3 types, 378 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.99→25 Å / Num. obs: 62306 / % possible obs: 98.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.039 / Rsym value: 0.099 / Net I/σ(I): 9.3
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 1.154 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4599 / CC1/2: 0.64 / Rpim(I) all: 0.565 / % possible all: 99.2

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Processing

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

Resolution: 1.99→24.173 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.86
RfactorNum. reflection% reflection
Rfree0.23 3014 4.84 %
Rwork0.1933 --
obs0.1951 62231 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→24.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 854 37 374 4732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174588
X-RAY DIFFRACTIONf_angle_d1.3646351
X-RAY DIFFRACTIONf_dihedral_angle_d22.6411805
X-RAY DIFFRACTIONf_chiral_restr0.087686
X-RAY DIFFRACTIONf_plane_restr0.008664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.02110.34531570.30452693X-RAY DIFFRACTION99
2.0211-2.05420.32121280.29452699X-RAY DIFFRACTION99
2.0542-2.08960.3571190.28262701X-RAY DIFFRACTION99
2.0896-2.12760.30991250.27152679X-RAY DIFFRACTION99
2.1276-2.16850.30261570.25752668X-RAY DIFFRACTION99
2.1685-2.21270.31771470.24662692X-RAY DIFFRACTION99
2.2127-2.26080.28571560.24592632X-RAY DIFFRACTION99
2.2608-2.31330.24021280.24142700X-RAY DIFFRACTION98
2.3133-2.37120.29271330.23332701X-RAY DIFFRACTION100
2.3712-2.43520.27781120.23842706X-RAY DIFFRACTION99
2.4352-2.50680.33411220.23362700X-RAY DIFFRACTION99
2.5068-2.58760.31241390.2362676X-RAY DIFFRACTION99
2.5876-2.680.27251620.23372698X-RAY DIFFRACTION99
2.68-2.78710.27071440.22912640X-RAY DIFFRACTION97
2.7871-2.91380.29531330.23472713X-RAY DIFFRACTION99
2.9138-3.06710.26581100.2252724X-RAY DIFFRACTION99
3.0671-3.25890.25431510.20142676X-RAY DIFFRACTION98
3.2589-3.50980.21751520.18682672X-RAY DIFFRACTION98
3.5098-3.86170.21941310.17212665X-RAY DIFFRACTION98
3.8617-4.41750.1791480.14442719X-RAY DIFFRACTION99
4.4175-5.55450.16161380.1412695X-RAY DIFFRACTION98
5.5545-24.17440.18491220.1692768X-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)
16.07580.1119-0.6941.4988-0.30651.0511-0.582-0.12750.808-0.05250.2939-0.1506-0.03120.05840.27360.31120.02840.00370.45530.06140.5179104.0073104.514431.057
22.22690.60140.94111.57810.42461.3467-0.1491-0.1227-0.29070.04450.17430.5513-0.0701-0.4528-0.02320.26110.0326-0.00850.40730.02520.443770.4812107.004730.1852
37.5833-1.203-1.67274.12391.97986.1692-0.7311-0.19441.140.59710.030.8438-0.04290.33390.69340.28770.00430.02230.658-0.04890.676460.254106.077633.2347
41.2944-0.66410.38211.9209-0.2450.7973-0.10260.2544-0.0370.0095-0.0148-0.289-0.01430.18390.09990.2787-0.02780.03230.36020.01520.377893.4078105.891529.8031
52.7765-0.2510.52561.5198-0.45832.45960.09880.1514-0.6062-0.2363-0.05280.12440.4194-0.0631-0.03760.4086-0.0069-0.03230.2715-0.06770.449283.881187.347223.2385
62.19650.31071.17631.65390.82433.20780.00510.08590.0448-0.2083-0.05620.1108-0.1469-0.23250.0480.461-0.0010.02440.32060.02960.259187.9461121.685613.3223
71.78020.167-0.59452.7089-0.46062.4668-0.0032-0.21350.07450.45760.01260.1226-0.1991-0.09260.00160.4269-0.0087-0.00620.3241-0.02570.235384.0064114.380843.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'B' and (resid 10 through 21 )
3X-RAY DIFFRACTION3chain 'C' and (resid 22 through 26 )
4X-RAY DIFFRACTION4chain 'C' and (resid 27 through 42 )
5X-RAY DIFFRACTION5chain 'I' and (resid 5 through 146 )
6X-RAY DIFFRACTION6chain 'I' and (resid 147 through 333 )
7X-RAY DIFFRACTION7chain 'I' and (resid 334 through 436 )

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