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- PDB-7d9y: DNA binding domain of human DNA Ligase IV mutant - A3V -

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Basic information

Entry
Database: PDB / ID: 7d9y
TitleDNA binding domain of human DNA Ligase IV mutant - A3V
ComponentsDNA ligase 4
KeywordsLIGASE / DBD mutant A3V / Native / ATP dependant ligase / hypomorphic mutant
Function / homology
Function and homology information


positive regulation of chromosome organization / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...positive regulation of chromosome organization / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / nucleotide-excision repair, DNA gap filling / single strand break repair / V(D)J recombination / double-strand break repair via classical nonhomologous end joining / isotype switching / positive regulation of neurogenesis / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / ligase activity / somatic stem cell population maintenance / response to X-ray / chromosome organization / condensed chromosome / neurogenesis / central nervous system development / stem cell proliferation / response to gamma radiation / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / base-excision repair / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / positive regulation of fibroblast proliferation / T cell differentiation in thymus / double-strand break repair / fibroblast proliferation / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / cell population proliferation / cell division / intracellular membrane-bounded organelle / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase IV domain / DNA ligase IV / 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 IV domain / DNA ligase IV / 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, 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsMaddi, E.R. / Raghavan, S.C. / Natesh, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/35/02/19/2009 India
CitationJournal: Protein Eng.Des.Sel. / Year: 2021
Title: Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability.
Authors: Maddi, E.R. / Raghavan, S.C. / Natesh, R.
History
DepositionOct 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase 4


Theoretical massNumber of molelcules
Total (without water)27,6561
Polymers27,6561
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Only one molecule in asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12230 Å2
Unit cell
Length a, b, c (Å)204.619, 204.619, 204.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein DNA ligase 4 / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4


Mass: 27655.990 Da / Num. of mol.: 1 / Mutation: A3V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Variant: Natural variant VAR 029352 / Plasmid: pENH240_A3V, pET15b
Details (production host): Site Directed Mutagenesis at nucleotide position 8 on pENH240
Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon Plus RIPL / References: UniProt: P49917, DNA ligase (ATP)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Description: Cubic crystals of DBD LigIV mutant - A3V exhibiting a characteristic bipyramidal shape. Actual dimensions of the largest crystal are of the order of 0.25 mm to 0.3 mm.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.125 M Tris pH 8.0, 20 % SOKALAN CP 42, 7.5% Methanol
Temp details: Rubarth Vibration Free Incubator at 4 Deg Centigrade

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2018 / Details: Beamline Optics OH1/OH3
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.76→39.38 Å / Num. obs: 9928 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 66.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.035 / Rrim(I) all: 0.143 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.76-2.91170.96214140.8140.2380.991100
8.74-39.3812.50.0413880.9980.0130.04399

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
Aimless0.7.2data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D9K

7d9k


Resolution: 2.76→39.38 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 473 4.79 %
Rwork0.2343 9394 -
obs0.2361 9867 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.3 Å2 / Biso mean: 66.7 Å2 / Biso min: 34.17 Å2
Refinement stepCycle: final / Resolution: 2.76→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 0 17 1737
Biso mean---55.38 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051750
X-RAY DIFFRACTIONf_angle_d0.7632366
X-RAY DIFFRACTIONf_chiral_restr0.053276
X-RAY DIFFRACTIONf_plane_restr0.007301
X-RAY DIFFRACTIONf_dihedral_angle_d11.2171074
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.76-3.250.33181650.27313034100
3.25-3.980.30191570.2463305599
3.98-39.380.24691510.21993305100

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