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- PDB-3jsl: Crystal structure of the adenylation domain of NAD+-dependent DNA... -

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Basic information

Entry
Database: PDB / ID: 3jsl
TitleCrystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus
ComponentsDNA ligase
KeywordsLIGASE / DNA ligase / NAD+-dependent / Staphylococcus aureus / DNA damage / DNA repair / DNA replication / Magnesium / Manganese / Metal-binding / NAD / Zinc
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / DNA binding / metal ion binding / cytosol
Similarity search - Function
Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation ...Dna Ligase; domain 1 - #70 / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Dna Ligase; domain 1 / Helix Hairpins / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHan, S. / Chang, J.S. / Griffor, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus.
Authors: Han, S. / Chang, J.S. / Griffor, M.
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA ligase
B: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,21810
Polymers73,4502
Non-polymers7698
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-117 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.152, 49.193, 88.039
Angle α, β, γ (deg.)90.10, 103.20, 90.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA ligase / Polydeoxyribonucleotide synthase [NAD+]


Mass: 36724.789 Da / Num. of mol.: 2 / Fragment: adenylation domain (UNP residues 1-312)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: LIGA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AIU7, DNA ligase (NAD+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.1-2.5M ammonium sulfate, 0.1M MES or HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 289K
PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 57629 / % possible obs: 95.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5146 / % possible all: 85.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.329 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25028 2930 5.1 %RANDOM
Rwork0.19573 ---
obs0.19843 54693 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-0.07 Å2-0.28 Å2
2---0.3 Å2-0.3 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 40 471 5499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9726912
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59225.036278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2391536
X-RAY DIFFRACTIONr_chiral_restr0.10.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23509
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2461
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.53147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42124960
X-RAY DIFFRACTIONr_scbond_it2.40632190
X-RAY DIFFRACTIONr_scangle_it3.6674.51952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 151 -
Rwork0.263 3162 -
obs--73.69 %

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