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- PDB-2q2t: Structure of Chlorella virus DNA ligase-adenylate bound to a 5' p... -

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Basic information

Entry
Database: PDB / ID: 2q2t
TitleStructure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick
Components
  • 5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
  • 5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3'
  • 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'
  • Chlorella virus DNA ligase
KeywordsLIGASE/DNA / LIGASE / LYSINE ADENYLATE / PROTEIN-DNA COMPLEX / LIGASE-DNA COMPLEX
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding
Similarity search - Function
DNA ligase, OB-like domain / DNA ligase OB-like domain / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins ...DNA ligase, OB-like domain / DNA ligase OB-like domain / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, conserved site / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA ligase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLima, C.D. / Nandakumar, J. / Nair, P.A. / Smith, P. / Shuman, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for nick recognition by a minimal pluripotent DNA ligase.
Authors: Nair, P.A. / Nandakumar, J. / Smith, P. / Odell, M. / Lima, C.D. / Shuman, S.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: 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: 5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'
D: 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'
A: Chlorella virus DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0525
Polymers49,7054
Non-polymers3471
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.301, 81.290, 96.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BD

#1: DNA chain 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: obtained synthetically / Details: Chemically synthesized.
#3: DNA chain 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: obtained synthetically / Details: Chemically synthesized.

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DNA/RNA hybrid / Protein , 2 types, 2 molecules CA

#2: DNA/RNA hybrid 5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'


Mass: 3035.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized.
#4: Protein Chlorella virus DNA ligase


Mass: 36833.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Strain: Chlorella virus / Gene: A544R / Plasmid: pET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O41026

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Non-polymers , 2 types, 146 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: A mixture of ChVLig (230 microM), nicked duplex DNA (220 microM) and 2 mM EDTA was added to an equal volume of a well solution containing 100 mM Bis-Tris-HCl (pH 6.5), 30 mM ammonium ...Details: A mixture of ChVLig (230 microM), nicked duplex DNA (220 microM) and 2 mM EDTA was added to an equal volume of a well solution containing 100 mM Bis-Tris-HCl (pH 6.5), 30 mM ammonium acetate, 22% PEG-4000. Crystals were grown at 22 C by the sitting-drop vapor diffusion method. Crystals appeared after 3 days. The crystals were transferred to buffer containing 100 mM Bis-Tris-HCl (pH 6.5), 30 mM ammonium acetate, 22% PEG-4000, 15% glycerol prior to flash-freezing in liquid nitrogen. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-Tris-HCL11
2ammonium acetate11
3PEG-400011
4EDTAEthylenediaminetetraacetic acid11
5PEG-400012
6EDTAEthylenediaminetetraacetic acid12
7ammonium acetate12
8ammonium acetate13
9EDTAEthylenediaminetetraacetic acid13
10PEG-400013
11glycerol13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 23844 / Num. obs: 23105 / % possible obs: 96.9 % / Observed criterion σ(I): -1.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Χ2: 1.05 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2248 / Χ2: 0.808 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVI

1fvi


Resolution: 2.3→38.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1201398.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1151 5 %RANDOM
Rwork0.214 ---
all-23815 --
obs-23077 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.819 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1--14.03 Å20 Å20 Å2
2--6.9 Å20 Å2
3---7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 858 22 145 3386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 162 4.3 %
Rwork0.3 3574 -
obs-3736 95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-apl.paramdna-rna-apc.top
X-RAY DIFFRACTION2dna-rna-apc_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.paramprotein-apl.top

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