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- PDB-6imj: The crystal structure of Se-AsfvLIG:DNA complex -

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Basic information

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


DNA ligase (ATP) activity / virion component / DNA recombination / DNA replication / 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 / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.554 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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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(*TP*C*CP*GP*GP*GP*AP*TP*GP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
D: DNA (5'-D(*C*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,23813
Polymers110,5144
Non-polymers1,7249
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-110 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.828, 63.099, 119.265
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA ligase / NP419L / PNP419L


Mass: 48514.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: NP419L, AFSV47Ss_0152 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E0U0

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*TP*C*CP*GP*GP*GP*AP*TP*GP*CP*TP*GP*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')


Mass: 6840.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*C*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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 87 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.23 Å3/Da / Density % sol: 61.9 %
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 100000.1 M Ammonium acetate, 0.1 M Cadmium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 44993 / % possible obs: 97.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 4370 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.554→29.936 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.2608 2279 5.07 %
Rwork0.2225 --
obs0.2245 44976 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.554→29.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 818 69 78 7253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057423
X-RAY DIFFRACTIONf_angle_d0.76510281
X-RAY DIFFRACTIONf_dihedral_angle_d18.8754228
X-RAY DIFFRACTIONf_chiral_restr0.0461153
X-RAY DIFFRACTIONf_plane_restr0.0051178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5541-2.60960.40281490.3562431X-RAY DIFFRACTION91
2.6096-2.67030.3551290.34052617X-RAY DIFFRACTION95
2.6703-2.7370.37061480.32422568X-RAY DIFFRACTION95
2.737-2.8110.41051350.32212600X-RAY DIFFRACTION96
2.811-2.89360.32491390.2832623X-RAY DIFFRACTION96
2.8936-2.9870.28021390.2792678X-RAY DIFFRACTION97
2.987-3.09360.30341390.2632614X-RAY DIFFRACTION98
3.0936-3.21730.30051580.24332658X-RAY DIFFRACTION98
3.2173-3.36360.25641220.22242731X-RAY DIFFRACTION98
3.3636-3.54060.23051400.20452695X-RAY DIFFRACTION99
3.5406-3.76210.26541440.20482685X-RAY DIFFRACTION99
3.7621-4.05190.21361540.18852710X-RAY DIFFRACTION99
4.0519-4.45850.2281270.17392741X-RAY DIFFRACTION99
4.4585-5.10090.19641440.1672747X-RAY DIFFRACTION99
5.1009-6.41610.22971610.20152773X-RAY DIFFRACTION100
6.4161-29.93820.24571510.20792826X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 33.8637 Å / Origin y: 2.0453 Å / Origin z: 29.919 Å
111213212223313233
T0.2791 Å20.009 Å2-0.0005 Å2-0.2795 Å2-0.05 Å2--0.2831 Å2
L0.0368 °2-0.0057 °20.0161 °2-0.1561 °2-0.1992 °2--0.1465 °2
S-0.0604 Å °-0.0031 Å °-0.011 Å °0.0024 Å °-0.0123 Å °-0.0056 Å °0.0158 Å °-0.0388 Å °0.0636 Å °
Refinement TLS groupSelection details: all

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