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- PDB-6imn: The crystal structure of AsfvLIG:CT2 complex -

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Basic information

Entry
Database: PDB / ID: 6imn
TitleThe crystal structure of AsfvLIG:CT2 complex
Components
  • DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
  • DNA ligase
KeywordsLIGASE/DNA / AsfvLIG with C:G complex / DNA BINDING PROTEIN / LIGASE-DNA complex
Function / homology
Function and homology information


DNA ligase (ATP) activity / virion component / DNA recombination / DNA replication / cell division / DNA repair / ATP binding
Similarity search - Function
: / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, conserved site / DNA ligase/mRNA capping enzyme / 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, OB-fold ...: / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, conserved site / DNA ligase/mRNA capping enzyme / 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, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, Y.Q. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues.
Authors: Chen, Y. / Liu, H. / Yang, C. / Gao, Y. / Yu, X. / Chen, X. / Cui, R. / Zheng, L. / Li, S. / Li, X. / Ma, J. / Huang, Z. / Li, J. / Gan, J.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase
B: DNA ligase
C: DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
D: DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
F: DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
G: DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5058
Polymers123,4346
Non-polymers712
Water1629
1
A: DNA ligase
F: DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
G: DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7534
Polymers61,7173
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-59 kcal/mol
Surface area24940 Å2
MethodPISA
2
B: DNA ligase
C: DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
D: DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7534
Polymers61,7173
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-55 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.235, 113.989, 243.068
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 / NP419L / PNP419L


Mass: 48233.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: NP419L / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E0U0
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')


Mass: 6643.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')


Mass: 6840.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 15% w/v PEG 10000, 0.1 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 44102 / % possible obs: 96.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2 / Num. unique obs: 3827 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YMJ

6ymj


Resolution: 2.7→29.937 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 27.48
RfactorNum. reflection% reflection
Rfree0.2682 1817 4.83 %
Rwork0.2473 --
obs0.2494 37640 82.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6438 1788 2 9 8237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048592
X-RAY DIFFRACTIONf_angle_d0.67912017
X-RAY DIFFRACTIONf_dihedral_angle_d20.6184809
X-RAY DIFFRACTIONf_chiral_restr0.0451334
X-RAY DIFFRACTIONf_plane_restr0.0051246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6982-2.77110.3802370.3667744X-RAY DIFFRACTION22
2.7711-2.85260.3931560.35251204X-RAY DIFFRACTION37
2.8526-2.94460.3976790.34311952X-RAY DIFFRACTION59
2.9446-3.04970.38751460.34992497X-RAY DIFFRACTION76
3.0497-3.17170.32751530.31512908X-RAY DIFFRACTION89
3.1717-3.31590.33251510.28173133X-RAY DIFFRACTION95
3.3159-3.49050.26381790.25943212X-RAY DIFFRACTION98
3.4905-3.70880.26681590.26443247X-RAY DIFFRACTION97
3.7088-3.99450.28471530.25123311X-RAY DIFFRACTION99
3.9945-4.39540.24221730.22583336X-RAY DIFFRACTION100
4.3954-5.02880.26411530.21163340X-RAY DIFFRACTION100
5.0288-6.32590.23451770.23473409X-RAY DIFFRACTION100
6.3259-29.93880.21912010.19853530X-RAY DIFFRACTION100

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