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- PDB-3pc7: X-ray crystal structure of the DNA ligase III-alpha BRCT domain. -

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Basic information

Entry
Database: PDB / ID: 3pc7
TitleX-ray crystal structure of the DNA ligase III-alpha BRCT domain.
ComponentsDNA ligase 3
KeywordsLIGASE / DNA repair / BRCT domain / Protein:protein interactions / XRCC1 BRCT2 domain / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / mitochondrial DNA repair ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / mitochondrial DNA repair / Resolution of AP sites via the single-nucleotide replacement pathway / DNA biosynthetic process / double-strand break repair via alternative nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / mitochondrion organization / double-strand break repair via homologous recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / cell division / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT 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 signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT 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 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. / BRCT domain / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Zinc finger, PARP-type / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCuneo, M.J. / Krahn, J.M. / London, R.E.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The structural basis for partitioning of the XRCC1/DNA ligase III-{alpha} BRCT-mediated dimer complexes.
Authors: Cuneo, M.J. / Gabel, S.A. / Krahn, J.M. / Ricker, M.A. / London, R.E.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase 3
B: DNA ligase 3


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water3,081171
1
A: DNA ligase 3

A: DNA ligase 3


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2
B: DNA ligase 3

B: DNA ligase 3


Theoretical massNumber of molelcules
Total (without water)20,0002
Polymers20,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)70.130, 70.130, 62.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1056-

HOH

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Components

#1: Protein DNA ligase 3 / DNA ligase III / Polydeoxyribonucleotide synthase [ATP] 3


Mass: 10000.187 Da / Num. of mol.: 2 / Fragment: unp residues 924-1009 / Mutation: C842S, C921S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG3 / Plasmid: pColaDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-RIL / References: UniProt: P49916, DNA ligase (ATP)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25 % polyethylene glycol 3350, 0.1 M BisTris, 0.25 M ammonium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793, 0.9748, 0.9795
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2010
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97481
30.97951
ReflectionResolution: 1.65→50 Å / Num. all: 19139 / Num. obs: 19139 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.069 / Χ2: 0.921 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.718.80.42218920.8541100
1.71-1.789.60.31318780.87199.9
1.78-1.869.60.21118950.868199.8
1.86-1.969.60.15319030.911199.8
1.96-2.089.50.11418870.985199.6
2.08-2.249.50.0919141.028199.4
2.24-2.469.60.07819030.973199.4
2.46-2.829.60.06419230.837198.8
2.82-3.559.10.06419341.023197.8
3.55-507.90.05520100.851195.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PC6

3pc6


Resolution: 1.65→46.589 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8969 / SU ML: 0.16 / σ(F): 0.95 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1808 5.09 %random
Rwork0.1401 ---
obs0.143 19117 99.3 %-
all-35544 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.065 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 84.28 Å2 / Biso mean: 29.361 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.0337 Å20 Å2-0 Å2
2--0.0337 Å2-0 Å2
3----0.0674 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 171 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081355
X-RAY DIFFRACTIONf_angle_d1.0991858
X-RAY DIFFRACTIONf_chiral_restr0.078206
X-RAY DIFFRACTIONf_plane_restr0.006243
X-RAY DIFFRACTIONf_dihedral_angle_d12.024498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6491-1.69360.20811420.142625862728100
1.6936-1.74350.21041360.137926432779100
1.7435-1.79980.22281520.123525842736100
1.7998-1.86410.1861430.11625932736100
1.8641-1.93870.17781290.117126402769100
1.9387-2.0270.20591470.116725892736100
2.027-2.13380.18441610.113526122773100
2.1338-2.26750.2041590.117925662725100
2.2675-2.44260.22881170.125426222739100
2.4426-2.68840.2081340.14392619275399
2.6884-3.07730.21571350.1522580271599
3.0773-3.87680.16461410.13872556269798
3.8768-46.60720.20241120.15432546265896

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