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- PDB-3vnn: Crystal Structure of a sub-domain of the nucleotidyltransferase (... -

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Basic information

Entry
Database: PDB / ID: 3vnn
TitleCrystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV
ComponentsDNA ligase 4
KeywordsLIGASE / DNA ligase / non-homologous end joining / DNA repair / XRCC4
Function / homology
Function and homology information


DNA ligation involved in DNA recombination / positive regulation of chromosome organization / 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 ...DNA ligation involved in DNA recombination / positive regulation of chromosome organization / 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 / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / V(D)J recombination / double-strand break repair via classical nonhomologous end joining / isotype switching / nucleotide-excision repair, DNA gap filling / 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 / 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 / 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 / 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 / DNA ligase/mRNA capping enzyme / 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 / DNA ligase/mRNA capping enzyme / 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 / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.903 Å
AuthorsOchi, T. / Wu, Q. / Chirgadze, D.Y. / Grossmann, J.G. / Bolanos-Garcia, V.M. / Blundell, T.L.
CitationJournal: Structure / Year: 2012
Title: Structural insights into the role of domain flexibility in human DNA ligase IV
Authors: Ochi, T. / Wu, Q. / Chirgadze, D.Y. / Grossmann, J.G. / Bolanos-Garcia, V.M. / Blundell, T.L.
History
DepositionJan 17, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase 4


Theoretical massNumber of molelcules
Total (without water)16,1971
Polymers16,1971
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.086, 39.086, 197.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 16196.514 Da / Num. of mol.: 1
Fragment: A sub-domain of the nucleotidyltransferase (adenylation) domain, UNP residues 268-405
Source method: isolated from a genetically manipulated source
Details: Hippocampus / Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pHAT5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49917, DNA ligase (ATP)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 7.5% PEG 6000, 100mM MES, 0.01mg/ml papain, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 3907 / Num. obs: 3860 / % possible obs: 98.8 % / Observed criterion σ(I): 2.5 / Redundancy: 11.9 % / Biso Wilson estimate: 89.06 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 15.3
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 5.19 / Rsym value: 0.544 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.903→30.64 Å / FOM work R set: 0.7276 / SU ML: 0.29 / σ(F): 1.33 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3049 381 10 %
Rwork0.2733 --
obs0.2767 3811 98.88 %
all-2263 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.262 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 109.8132 Å2
Baniso -1Baniso -2Baniso -3
1-8.8971 Å20 Å2-0 Å2
2--8.8971 Å20 Å2
3----17.7942 Å2
Refinement stepCycle: LAST / Resolution: 2.903→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 0 3 952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014970
X-RAY DIFFRACTIONf_angle_d1.9711319
X-RAY DIFFRACTIONf_dihedral_angle_d18.975331
X-RAY DIFFRACTIONf_chiral_restr0.156147
X-RAY DIFFRACTIONf_plane_restr0.011173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9028-3.32240.39091210.30421100X-RAY DIFFRACTION100
3.3224-4.18420.29781260.25811127X-RAY DIFFRACTION100
4.1842-30.64130.2921340.27421203X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -0.1544 Å / Origin y: 12.152 Å / Origin z: 62.2802 Å
111213212223313233
T1.1422 Å2-0.5319 Å20.4325 Å2-0.6554 Å2-0.1712 Å2--0.6698 Å2
L3.3707 °2-0.9543 °21.4246 °2-1.3123 °20.7508 °2--2.7432 °2
S0.3848 Å °0.0965 Å °0.1399 Å °-0.0758 Å °0.1461 Å °0.004 Å °-1.1068 Å °0.6403 Å °-0.2819 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA268 - 406
2X-RAY DIFFRACTION1allA501 - 503

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