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- PDB-8ak4: Structure of the C-terminally truncated NAD+-dependent DNA ligase... -

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Basic information

Entry
Database: PDB / ID: 8ak4
TitleStructure of the C-terminally truncated NAD+-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans
ComponentsDNA ligase
KeywordsDNA BINDING PROTEIN / DNA ligase A / BRCT / DNA nick-joining
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / metal ion binding / cytosol
Similarity search - Function
Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / 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 ...Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / 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 / RuvA domain 2-like / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
AuthorsFernandes, A. / Williamson, A.K. / Matias, P.M. / Moe, E.
Funding support Portugal, New Zealand, 6items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)UIDB/04612/2020 Portugal
Foundation for Science and Technology (FCT)LA/P/0087/2020 Portugal
Foundation for Science and Technology (FCT)PTDC/BBB-BEP/0561/2014 Portugal
Foundation for Science and Technology (FCT)SFRH/BPD/97493/2013 Portugal
Foundation for Science and Technology (FCT)PD/BD/13548/2018 Portugal
Marsden Fund18-UOW-034 New Zealand
CitationJournal: Extremophiles / Year: 2023
Title: Structure/function studies of the NAD + -dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding.
Authors: Fernandes, A. / Williamson, A. / Matias, P.M. / Moe, E.
History
DepositionJul 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0307
Polymers65,6591
Non-polymers3726
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-86 kcal/mol
Surface area24350 Å2
Unit cell
Length a, b, c (Å)70.844, 73.434, 149.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA ligase / / Polydeoxyribonucleotide synthase [NAD(+)]


Mass: 65658.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: ligA, DR_2069 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3* / References: UniProt: Q9RSQ5, DNA ligase (NAD+)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.7 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate pH 6.5, 20 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2021 / Details: KB focusing mirrors
RadiationMonochromator: channell-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.36→149.94 Å / Num. obs: 7848 / % possible obs: 67.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 110.08 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.12 / Net I/σ(I): 5.7
Reflection shellResolution: 3.36→3.65 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 393 / CC1/2: 0.442 / Rpim(I) all: 0.739 / % possible all: 15.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5 (20200918)data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: From AlphaFold2

Resolution: 3.36→74.97 Å / SU ML: 0.5011 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Hydrogen atoms were added in calculated positions with the PHENIX.READYSET tool. Isotropic displacement parameters (ADPs) were refined for all non-hydrogen atoms. TLS rigid body refinement ...Details: Hydrogen atoms were added in calculated positions with the PHENIX.READYSET tool. Isotropic displacement parameters (ADPs) were refined for all non-hydrogen atoms. TLS rigid body refinement of anisotropic ADPs was performed in the final refinement cycles using three rigid body groups for the protein chain, estimated by PHENIX from a prior fully isotropic refinement. Relative X-ray/stereochemistry and X-ray/ADP weights were optimized to reduce the gap between R-work and R-free.
RfactorNum. reflection% reflection
Rfree0.2751 393 5.03 %
Rwork0.215 7420 -
obs0.2182 7813 66.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.68 Å2
Refinement stepCycle: LAST / Resolution: 3.36→74.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 6 0 3932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024002
X-RAY DIFFRACTIONf_angle_d0.48665433
X-RAY DIFFRACTIONf_chiral_restr0.0393611
X-RAY DIFFRACTIONf_plane_restr0.0042722
X-RAY DIFFRACTIONf_dihedral_angle_d12.21641486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.840.4556440.3031105X-RAY DIFFRACTION30.91
3.91-4.850.28731630.2382909X-RAY DIFFRACTION88.66
4.85-74.970.25471860.19323406X-RAY DIFFRACTION89.29
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)
12.149870982481.5490283517-1.079060587143.63037100522-0.1068770446051.46860320456-0.019213025540.3491207136820.225577327162-0.1217393760030.03853271884620.342404772662-0.1680294964010.1865522934960.01474816394230.8171807394890.0587921799476-0.1296416351070.7352073163420.04057129301040.7427908672617.4829634570731.832991215230.6109859965
21.11890949909-0.144868522135-0.7027603760342.15891333351-1.693589839441.892770188150.07477405670230.0561173158094-0.1660161676170.195867594713-0.709109280932-0.304945952006-0.3209762251360.7328452805620.5033479769210.90232334877-0.239877893292-0.1387238358351.020393156280.07481413234160.83952317768313.374418524119.252543127263.5110445702
32.60992755671.71330806964-0.2990491345564.36601774178-0.8940544123732.689905495630.0442985667565-0.0402511354065-0.555047456897-0.290538725409-0.128212565969-0.01228124679930.4855346469360.1383070339220.03296282740871.00358358840.0109725540261-0.08282921708340.638586312739-0.008567922354940.673273215725-7.45263622979-6.5442505572660.6277316889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 81 through 328 )81 - 3281 - 248
22chain 'A' and (resid 329 through 436 )329 - 436249 - 356
33chain 'A' and (resid 437 through 593 )437 - 593357 - 513

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