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- PDB-6dt1: Crystal structure of the ligase from bacteriophage T4 complexed w... -

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Basic information

Entry
Database: PDB / ID: 6dt1
TitleCrystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate
Components
  • DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3')
  • DNA (5'-D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA ligase
KeywordsLIGASE/DNA / LIGASE-DNA COMPLEX / LIGASE
Function / homology
Function and homology information


DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding / metal ion 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, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095558 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Authors: Shi, K. / Bohl, T.E. / Park, J. / Zasada, A. / Malik, S. / Banerjee, S. / Tran, V. / Li, N. / Yin, Z. / Kurniawan, F. / Orellana, K. / Aihara, H.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 10, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conn / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.label_seq_id / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_seq_id
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 11, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,64131
Polymers140,7378
Non-polymers2,90423
Water4,810267
1
A: DNA ligase
B: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3')
C: DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3')
D: DNA (5'-D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,89025
Polymers70,3684
Non-polymers2,52221
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-80 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.526, 67.429, 114.635
Angle α, β, γ (deg.)88.78, 80.94, 62.97
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AE

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


Mass: 57540.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 30 / Production host: Escherichia coli (E. coli) / References: UniProt: P00970, DNA ligase (ATP)

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DNA chain , 3 types, 6 molecules BFCGDH

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


Mass: 3349.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T4 (virus)
#3: DNA chain DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3')


Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T4 (virus)
#4: DNA chain DNA (5'-D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6393.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T4 (virus)

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Non-polymers , 7 types, 290 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O2S2
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→113.572 Å / Num. obs: 42792 / % possible obs: 98.6 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4259 / CC1/2: 0.622 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x9n

1x9n


Resolution: 2.75→113.021 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 2154 5.04 %
Rwork0.1698 --
obs0.1723 42747 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→113.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 1708 177 267 9514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069564
X-RAY DIFFRACTIONf_angle_d0.79613196
X-RAY DIFFRACTIONf_dihedral_angle_d18.025510
X-RAY DIFFRACTIONf_chiral_restr0.0471470
X-RAY DIFFRACTIONf_plane_restr0.0041371
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)
12.35770.20440.19552.06370.58432.9804-0.05880.20720.4899-0.0010.1970.434-0.2194-0.4999-0.01020.24930.10990.14020.35260.15750.5325-65.8212-51.2927-48.6039
22.0217-0.202-0.52961.9746-0.28470.64950.0373-0.1557-0.24570.2528-0.0512-0.04480.03990.05040.00210.33590.00430.0580.20380.08230.3907-50.6478-76.4121-36.7964
31.91560.57050.26272.158-0.92253.6826-0.12060.1273-0.5073-0.139-0.0286-0.22570.4433-0.20490.13440.4020.01870.05380.12580.01020.4805-50.9621-82.8686-43.1231
41.66990.9464-0.55732.1809-0.47740.76880.0724-0.1121-0.24580.2785-0.0901-0.32780.08520.1670.01260.27520.0648-0.0190.25980.05020.4031-37.7203-68.6647-39.1809
55.2883-1.4778-0.85852.4091-0.36532.8562-0.13730.4574-0.0933-0.34340.1146-0.52760.19870.19090.03770.2260.03280.07470.3223-0.00210.4576-28.0225-58.4085-54.2364
62.5574-0.46931.580.23110.50627.46040.361-0.7708-0.9164-0.03040.03950.14951.31-0.162-0.37941.5703-0.2959-0.35911.18760.31460.7959-58.9071-106.459419.7056
73.31870.5186-0.00841.7143-0.24164.58810.3429-0.66470.31540.2333-0.11730.3947-0.3378-0.7829-0.21770.74990.1111-0.03530.8035-0.05590.5019-67.6014-80.41322.3064
88.256-2.0710.76244.6097-4.35874.47450.43760.03550.0993-0.0414-0.5632-0.4376-0.0391.16770.05870.71060.0317-0.18750.8888-0.03050.458-41.5635-82.0276-5.0037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 125 )
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 291 )
4X-RAY DIFFRACTION4chain 'A' and (resid 292 through 421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 487 )
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 125 )
7X-RAY DIFFRACTION7chain 'E' and (resid 126 through 421 )
8X-RAY DIFFRACTION8chain 'E' and (resid 422 through 487 )

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