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- PDB-3rr5: DNA ligase from the archaeon Thermococcus sp. 1519 -

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Basic information

Entry
Database: PDB / ID: 3rr5
TitleDNA ligase from the archaeon Thermococcus sp. 1519
ComponentsDNA ligase
KeywordsLIGASE / ATP-dependent thermostable DNA ligase / Archaeon
Function / homology
Function and homology information


DNA ligase (ATP or NAD+) / DNA ligation involved in DNA repair / DNA ligase (ATP) activity / DNA biosynthetic process / DNA recombination / DNA replication / cell cycle / cell division / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA ligase, ATP-dependent, bacterial/archaeal / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase/mRNA capping enzyme ...DNA ligase, ATP-dependent, bacterial/archaeal / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus sp. 1519 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.018 Å
AuthorsPetrova, T. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / Popov, V.O. / Polyakov, K.M. / Ravin, N.V. / Shabalin, I.G. / Skryabin, K.G. / Stekhanova, T.N. / Kovalchuk, M.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.
Authors: Petrova, T. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / Polyakov, K.M. / Volkov, V.V. / Kozin, M. / Ravin, N.V. / Shabalin, I.G. / Skryabin, K.G. / Stekhanova, T.N. / Kovalchuk, M.V. / Popov, V.O.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9162
Polymers64,8921
Non-polymers241
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.950, 85.600, 105.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA ligase / / Polydeoxyribonucleotide synthase [ATP]


Mass: 64891.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. 1519 (archaea) / Strain: 1519 / Gene: lig / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): DLT1270/pRARE-2 / References: UniProt: C0LJI8, DNA ligase (ATP)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 7.5
Details: 0.1 Na Cacodilate, 0.2 M MgCl2, 20% Glicerol, 16% PEG 8000, 100 mM NaCl, 50mM Tris-HCl, Protein 22mg/mL (protein buffer: 50mM Tris-Hcl, 100 mM NaCl, 0.5 DTT), Gel-tube counter-diffusion ...Details: 0.1 Na Cacodilate, 0.2 M MgCl2, 20% Glicerol, 16% PEG 8000, 100 mM NaCl, 50mM Tris-HCl, Protein 22mg/mL (protein buffer: 50mM Tris-Hcl, 100 mM NaCl, 0.5 DTT), Gel-tube counter-diffusion method, pH 7.5, LIQUID DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2010 / Details: The rhodium-coated mirrors
RadiationMonochromator: The rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 3→29.257 Å / Num. all: 14557 / Num. obs: 14237 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Net I/σ(I): 25.09
Reflection shellResolution: 3.02→3.2 Å / Mean I/σ(I) obs: 3.43 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3GDE

3gde


Resolution: 3.018→29.257 Å / SU ML: 0.9 / σ(F): 1.35 / Phase error: 31.58 / Stereochemistry target values: ML / Details: two B-factors per residues
RfactorNum. reflection% reflection
Rfree0.3096 715 5.02 %
Rwork0.2326 --
obs0.2365 14229 99.69 %
all-14237 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.937 Å2 / ksol: 0.284 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2354 Å2-0 Å20 Å2
2---5.8688 Å20 Å2
3---13.1043 Å2
Refinement stepCycle: LAST / Resolution: 3.018→29.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 1 4 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094191
X-RAY DIFFRACTIONf_angle_d1.3195679
X-RAY DIFFRACTIONf_dihedral_angle_d18.7681527
X-RAY DIFFRACTIONf_chiral_restr0.086659
X-RAY DIFFRACTIONf_plane_restr0.006739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0183-3.2510.37751550.33422611X-RAY DIFFRACTION99
3.251-3.57770.31841490.26062663X-RAY DIFFRACTION100
3.5777-4.09420.35061350.23812694X-RAY DIFFRACTION100
4.0942-5.15360.26581290.20032722X-RAY DIFFRACTION100
5.1536-29.25830.30231470.22592824X-RAY DIFFRACTION99

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