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- PDB-3n9d: Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain -

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Basic information

Entry
Database: PDB / ID: 3n9d
TitleMonoclinic Structure of P. aeruginosa LigD phosphoesterase domain
ComponentsProbable ATP-dependent DNA ligase
KeywordsLIGASE / Phosphoesterase / Metalloenzyme / NHEJ / Manganese / Beta Barrel
Function / homology
Function and homology information


RNA exonuclease activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA biosynthetic process / nucleotidyltransferase activity / DNA recombination / DNA-directed DNA polymerase activity / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA ligase D / LigD polymerase domain, PaeLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. ...DNA ligase D / LigD polymerase domain, PaeLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / YTTRIUM (III) ION / Multifunctional non-homologous end joining protein LigD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShuman, S. / Nair, P. / Smith, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily
Authors: Nair, P.A. / Smith, P. / Shuman, S.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9006
Polymers19,4751
Non-polymers4255
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.997, 56.585, 43.503
Angle α, β, γ (deg.)90.00, 118.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-189-

YT3

DetailsThis protein is monomeric in solution and a single protomer occupies the asymmetric unit of this crystal lattice.

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Components

#1: Protein Probable ATP-dependent DNA ligase


Mass: 19474.963 Da / Num. of mol.: 1 / Fragment: Phosphoesterase Domain
Source method: isolated from a genetically manipulated source
Details: pET28b plasmid expressing His10-tagged-Smt3 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: NP_250828.1, PA2138 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL+ / References: UniProt: Q9I1X7
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ;Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG ...Details: ;Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG 5000 monomethylether (MME) (20 - 30%), 100 mM 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.8 - 7.0, 200 mM ammonium sulfate, and 10 mM yttrium (III) chloride at 22 C. , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 20, 2010 / Details: Osmic Confocal Mirrors
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 8818 / Num. obs: 8792 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.103 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.97 / Num. unique all: 458 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A of PDB entry 3N9B

3n9b


Resolution: 2.3→28.293 Å / SU ML: 0.33 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 930 10.65 %10% of data selected at random using CCP4/Unique
Rwork0.2117 ---
obs0.2171 8730 99.7 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.121 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.658 Å20 Å2-4.5695 Å2
2---9.94 Å2-0 Å2
3---16.4482 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 13 85 1285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021235
X-RAY DIFFRACTIONf_angle_d0.6381673
X-RAY DIFFRACTIONf_dihedral_angle_d13.379456
X-RAY DIFFRACTIONf_chiral_restr0.048173
X-RAY DIFFRACTIONf_plane_restr0.002217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.42130.30661410.23981106X-RAY DIFFRACTION100
2.4213-2.57290.27191470.22041079X-RAY DIFFRACTION99
2.5729-2.77140.30361380.21981088X-RAY DIFFRACTION100
2.7714-3.050.29361230.22171122X-RAY DIFFRACTION100
3.05-3.49070.28541230.22071125X-RAY DIFFRACTION100
3.4907-4.39520.23581310.19521126X-RAY DIFFRACTION100
4.3952-28.29460.20311270.18251154X-RAY DIFFRACTION100

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