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- PDB-1z56: Co-Crystal Structure of Lif1p-Lig4p -

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Basic information

Entry
Database: PDB / ID: 1z56
TitleCo-Crystal Structure of Lif1p-Lig4p
Components
  • (Ligase interacting factor ...) x 8
  • DNA ligase IV
KeywordsLIGASE / DNA Repair / BRCT / NHEJ / Xrcc4 / DNA Ligase / Coiled-coil
Function / homology
Function and homology information


DNA ligase IV complex / maintenance of rDNA / DNA ligase (ATP) / DNA ligase (ATP) activity / nucleotide-excision repair, DNA gap filling / double-strand break repair via classical nonhomologous end joining / DNA biosynthetic process / double-strand break repair via nonhomologous end joining / DNA recombination / cell division ...DNA ligase IV complex / maintenance of rDNA / DNA ligase (ATP) / DNA ligase (ATP) activity / nucleotide-excision repair, DNA gap filling / double-strand break repair via classical nonhomologous end joining / DNA biosynthetic process / double-strand break repair via nonhomologous end joining / DNA recombination / cell division / chromatin binding / chromatin / DNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA ligase 4 / DNA Ligase 4, adenylation 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, conserved site ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA ligase 4 / DNA Ligase 4, adenylation 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / BRCT domain / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / BRCT domain / DNA repair protein XRCC4-like, C-terminal / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nucleic acid-binding, OB-fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-homologous end-joining factor LIF1 / DNA ligase 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.92 Å
AuthorsDore, A.S. / Furnham, N. / Davies, O.R. / Sibanda, B.L. / Chirgadze, D.Y. / Jackson, S.P. / Pellegrini, L. / Blundell, T.L.
CitationJournal: DNA REPAIR / Year: 2006
Title: Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.
Authors: Dore, A.S. / Furnham, N. / Davies, O.R. / Sibanda, B.L. / Chirgadze, D.Y. / Jackson, S.P. / Pellegrini, L. / Blundell, T.L.
History
DepositionMar 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 999 SEQUENCE As stated by the authors, the residues in chains D,E, F,G,H,I,J,K could not be aligned ... SEQUENCE As stated by the authors, the residues in chains D,E, F,G,H,I,J,K could not be aligned with any region of the two chains A and B due to low electron density and therefore have been labeled UNK.
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DEFINED
Remark 700 SHEET DETERMINATION METHOD: AUTHOR DEFINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ligase interacting factor 1
B: Ligase interacting factor 1
C: DNA ligase IV
D: Ligase interacting factor 1
E: Ligase interacting factor 1
F: Ligase interacting factor 1
G: Ligase interacting factor 1
H: Ligase interacting factor 1
I: Ligase interacting factor 1
J: Ligase interacting factor 1
K: Ligase interacting factor 1


Theoretical massNumber of molelcules
Total (without water)102,07211
Polymers102,07211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.617, 247.617, 98.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Ligase interacting factor ... , 8 types, 10 molecules ABDEHFGIJK

#1: Protein Ligase interacting factor 1


Mass: 28674.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P53150
#3: Protein/peptide Ligase interacting factor 1


Mass: 698.854 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)
#4: Protein/peptide Ligase interacting factor 1


Mass: 613.749 Da / Num. of mol.: 2 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)
#5: Protein/peptide Ligase interacting factor 1


Mass: 3847.734 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)
#6: Protein/peptide Ligase interacting factor 1


Mass: 3166.895 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)
#7: Protein/peptide Ligase interacting factor 1


Mass: 2571.161 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)
#8: Protein/peptide Ligase interacting factor 1


Mass: 1720.111 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)
#9: Protein/peptide Ligase interacting factor 1


Mass: 1124.378 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIF1 / Production host: Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules C

#2: Protein DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] / DNA ligase IV homolog


Mass: 30366.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DNL4, LIG4 / Plasmid: pGAT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q08387, DNA ligase (ATP)

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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: 5 Å3/Da / Density % sol: 75.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl, Sodium Chloride, Dithiothreitol, PEG 6000, 2-(N-morpholino)ethanesulfonic acid, Ethylene Glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.968
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2004 / Details: SI-111 DOUBLE MONOCHROMATOR
RadiationMonochromator: SI-111 DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 3.92→49.2 Å / Num. all: 16493 / Num. obs: 16475 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 10.1 % / Rmerge(I) obs: 0.175 / Rsym value: 0.175 / Net I/σ(I): 5.7
Reflection shellResolution: 3.92→3.99 Å / Rmerge(I) obs: 0.799 / Rsym value: 0.799 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.92→49.2 Å / Cor.coef. Fo:Fc: 0.75 / Cor.coef. Fo:Fc free: 0.659 / SU B: 70.148 / SU ML: 1.06 / Cross valid method: THROUGHOUT / ESU R Free: 0.961 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.467 832 5.1 %RANDOM
Rwork0.4 ---
obs0.403 15638 99.8 %-
all-15638 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.705 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.65 Å20 Å2
2--1.31 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 3.92→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 0 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214198
X-RAY DIFFRACTIONr_bond_other_d0.0120.028
X-RAY DIFFRACTIONr_angle_refined_deg2.131.985623
X-RAY DIFFRACTIONr_angle_other_deg1.987316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1665545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91424.241158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.97115809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9121531
X-RAY DIFFRACTIONr_chiral_restr0.1320.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023049
X-RAY DIFFRACTIONr_gen_planes_other0.0050.028
X-RAY DIFFRACTIONr_nbd_refined0.330.22550
X-RAY DIFFRACTIONr_nbd_other0.3230.218
X-RAY DIFFRACTIONr_nbtor_refined0.3240.22748
X-RAY DIFFRACTIONr_nbtor_other0.2540.216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5961.52848
X-RAY DIFFRACTIONr_mcbond_other0.0941.58
X-RAY DIFFRACTIONr_mcangle_it1.04224463
X-RAY DIFFRACTIONr_scbond_it1.20331502
X-RAY DIFFRACTIONr_scangle_it2.1514.51160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.92→4.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 67 -
Rwork0.361 1105 -
obs--99.07 %

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