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- PDB-1ik9: CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ik9
TitleCRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
Components
  • DNA LIGASE IV
  • DNA REPAIR PROTEIN XRCC4
KeywordsGENE REGULATION/LIGASE / DNA end joining / double-strand break repair / V(D)J recombination / protein-protein complex / coiled coil / GENE REGULATION-LIGASE COMPLEX
Function / homology
Function and homology information


DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination ...DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / nucleotide-excision repair, DNA gap filling / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / protein localization to site of double-strand break / V(D)J recombination / isotype switching / double-strand break repair via classical nonhomologous end joining / positive regulation of neurogenesis / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / somatic stem cell population maintenance / ligase activity / response to X-ray / chromosome organization / SUMOylation of DNA damage response and repair proteins / condensed chromosome / neurogenesis / central nervous system development / stem cell proliferation / cellular response to ionizing radiation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / double-strand break repair / positive regulation of fibroblast proliferation / site of double-strand break / T cell differentiation in thymus / fibroblast proliferation / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / chromosome, telomeric region / cell cycle / cell division / intracellular membrane-bounded organelle / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / 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 signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase 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 / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nucleic acid-binding, OB-fold / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA ligase 4 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 2.3 Å
AuthorsSibanda, B.L. / Critchlow, S.E. / Begun, J. / Pei, X.Y. / Jackson, S.P. / Blundell, T.L. / Pellegrini, L.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of an Xrcc4-DNA ligase IV complex.
Authors: Sibanda, B.L. / Critchlow, S.E. / Begun, J. / Pei, X.Y. / Jackson, S.P. / Blundell, T.L. / Pellegrini, L.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN XRCC4
B: DNA REPAIR PROTEIN XRCC4
C: DNA LIGASE IV


Theoretical massNumber of molelcules
Total (without water)53,2573
Polymers53,2573
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-58 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.062, 79.628, 242.142
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 REPAIR PROTEIN XRCC4 /


Mass: 24466.619 Da / Num. of mol.: 2 / Fragment: XRCC4 FRAGMENT, RESIDUES 1-213 / Mutation: C93A,C128A,C130A,C165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pET15a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13426
#2: Protein/peptide DNA LIGASE IV / / POLYDEOXYRIBONUCLEOTIDE SYNTHASE


Mass: 4323.684 Da / Num. of mol.: 1 / Fragment: LINKER CONNECTING BRCT DOMAINS, RESIDUES 748-784
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pTYB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49917, DNA ligase (ATP)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 4.3 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, MES, xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.050 mMprotein1drop
210 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
41.5 %(w/v)PEG60001drop
50.05 MMES1droppH6.0
71.5 %(w/v)xylitol precipitant solution1drop
86 %(w/v)PEG60001reservoir
90.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2001 / Details: mirrors
RadiationMonochromator: 111/311 Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→33.26 Å / Num. all: 34224 / Num. obs: 34224 / % possible obs: 85.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.3 / Num. unique all: 795 / Rsym value: 0.229 / % possible all: 44.4
Reflection
*PLUS
Num. measured all: 72477
Reflection shell
*PLUS
% possible obs: 44.4 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAS / Resolution: 2.3→33.26 Å / Isotropic thermal model: overall anisotropic B value / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1723 -random
Rwork0.228 ---
all-34084 --
obs-34084 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.1307 Å2 / ksol: 0.340363 e/Å3
Displacement parametersBiso mean: 70.4 Å2
Baniso -1Baniso -2Baniso -3
1-35.06 Å2-12.72 Å222.34 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 0 224 3736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.45
X-RAY DIFFRACTIONc_mcbond_it3.6
X-RAY DIFFRACTIONc_scbond_it6.41
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.048
RfactorNum. reflection% reflection
Rfree0.467 95 -
Rwork0.466 --
obs-1980 50.4 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 70.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.45
X-RAY DIFFRACTIONc_mcbond_it3.6
X-RAY DIFFRACTIONc_scbond_it6.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.467 / Rfactor Rwork: 0.466

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