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- PDB-7d9k: DNA binding domain of human DNA Ligase IV - Wild type -

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Basic information

Entry
Database: PDB / ID: 7d9k
TitleDNA binding domain of human DNA Ligase IV - Wild type
ComponentsDNA ligase 4
KeywordsLIGASE / DBD / Native / ATP dependant ligase.
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 / nonhomologous end joining complex ...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 / nonhomologous end joining complex / immunoglobulin V(D)J recombination / 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 / cellular response to lithium ion / DNA biosynthetic process / 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 / cellular response to ionizing radiation / response to gamma 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 / double-strand break repair / T cell differentiation in thymus / fibroblast proliferation / neuron apoptotic process / negative regulation of neuron apoptotic process / in utero embryonic development / 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 / molecular replacement / Resolution: 2.9 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 13, 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)27,6281
Polymers27,6281
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12100 Å2
Unit cell
Length a, b, c (Å)202.869, 202.869, 202.869
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: 27627.938 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pET15b, pENH240
Details (production host): DBDLigIV cloned at NdeI and BamHI restriction site in pET15b
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.: 21 / 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: 61.33 %
Description: Cubic crystals of DBD LigIV-Wt exhibiting a characteristic bipyramidal shape. Actual dimensions of the largest crystal are of the order of 0.25 um to 0.26 mm.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 20 % SOKALAN CP 42, 5% Methanol / Temp details: Rubarth Incubator Vibration Free

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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: 0.97927 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2018 / Details: Beamline Optics OH1/OH3
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.9→39.042 Å / Num. obs: 8410 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 61.81 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.349 / Rpim(I) all: 0.092 / Rrim(I) all: 0.362 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.0816.21.33513130.7060.3411.378100
8.7-39.04110.133810.9160.0420.13899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
MOLREP11.6.04phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HTO

4hto


Resolution: 2.9→39.04 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2988 433 5.19 %
Rwork0.2563 7911 -
obs0.2584 8344 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.1 Å2 / Biso mean: 63.8416 Å2 / Biso min: 27.54 Å2
Refinement stepCycle: final / Resolution: 2.9→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 0 21 1713
Biso mean---49.35 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031720
X-RAY DIFFRACTIONf_angle_d0.5672326
X-RAY DIFFRACTIONf_chiral_restr0.039274
X-RAY DIFFRACTIONf_plane_restr0.003296
X-RAY DIFFRACTIONf_dihedral_angle_d11.331054
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.180.37351510.29752555100
3.3204-4.18250.31831290.2655257498
4.18-39.040.26341530.23812782100

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